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  List of publications in data science

  This is a list of publications in data science, generally organized by order of use in a data analysis workflow. See the list of publications in statistics for more research-based and fundamental publications; while this list is more applied, business oriented, and cross-disciplinary. General article inclusion criteria are: Papers from notable practitioners or notable professors, either with a Wikipedia page or reference to their notability Common knowledge all data professionals should know, with references validating this claim Highly cited applied statistics and machine learning publications Discussion-facilitating papers on the field of data science as a whole (for example, the Attention Is All You Need paper is arguably a landmark paper that can be added here, but it is specific to generative artificial intelligence, not for all practitioners of data) Some reasons why a particular publication might be regarded as important: Topic creator – A publication that created a new topic Breakthrough – A publication that changed scientific knowledge significantly Influence – A publication which has significantly influenced the world or has had a massive impact on the teaching of data science. When possible, a reference is used to validate the inclusion of the publication in this list. == History == Statistical Modeling: The Two Cultures (with comments and a rejoinder by the author) Author: Leo Breiman Publication data: Online version: https://projecteuclid.org/journals/statistical-science/volume-16/issue-3/Statistical-Modeling--The-Two-Cultures-with-comments-and-a/10.1214/ss/1009213726.pdf Description: Describes two cultures of statistics, one using a parsimonious and generative stochastic model, while the other is an algorithmic model with no known mechanism for how the data is generated. Breiman argues that while statistics has traditionally favored using the stochastic model, there is value in expanding the methods that statisticians can use to study phenomenon. Importance: Influence on the philosophies of statisticians right before the increased use of machine learning and deep learning methods. In a 20-year retrospective on this article, "Breiman's words are perhaps more relevant than ever". Notable statisticians at the time wrote opinion pieces about the publication. Although overall critical of the publication, David Cox writes that the publication "contains enough truth and exposes enough weaknesses to be thought-provoking." Bradley Efron commented that this publication is a "stimulating paper". Emanuel Parzen also comments about this publication that "Breiman alerts us to systematic blunders (leading to wrong conclusions) that have been committed applying current statistical practice of data modeling". Data Scientist: The Sexiest Job of the 21st Century Author: Thomas H. Davenport and DJ Patil Publication data: Online version: hbr.org/2022/07/is-data-scientist-still-the-sexiest-job-of-the-21st-century Description: Describes the new role at companies that is coined "Data scientist", what they do, how an organization might recruit one to their organization, and how to work with one effectively. Importance: This publication has been an influence on the data community as mentioned near the time it was published in 2012 by institutions like IEEE Spectrum, but also mentioned nearly a decade later asking the same question the title poses. In a retrospective response to their own publication 10 years earlier, authors Davenport and Patil have reflected that the role of a data scientist has "become better institutionalized, the scope of the job has been redefined, the technology it relies on has made huge strides, and the importance of non-technical expertise, such as ethics and change management, has grown". 50 Years of Data Science Author: David Donoho Publication data: Online version: https://www.tandfonline.com/doi/full/10.1080/10618600.2017.1384734 Description: Retrospective discussion paper on the history and origins of data science, with a number of commentary from notable statisticians. Importance: This has been described as "the first in the field to present such a comprehensive and in-depth survey and overview", and helps to define the field that has many definitions. The Composable Data Management System Manifesto Author: Pedro Pedreira, Orri Erling, Konstantinos Karanasos, Scott Schneider, Wes McKinney, Satya R Valluri, Mohamed Zait, Jacques Nadeau Publication data: Online version: https://www.vldb.org/pvldb/vol16/p2679-pedreira.pdf Description: The vision paper advocating for a paradigm shift in how data management systems are designed using standard, composable, interoperable tools rather than siloed software tools. Importance: A paradigm shifting view on how future data science software tools should be designed for more efficient workflows, the principles of which "will be especially crucial for addressing fragmentation, improving interoperability, and promoting user-centricity as data ecosystems grow increasingly complex". == Data collection and organization == Tidy Data Author: Hadley Wickham Publication data: Online version: https://www.jstatsoft.org/article/view/v059i10/ https://vita.had.co.nz/papers/tidy-data.pdf Description: Describes a framework for data cleaning that is summarized in the quote, "each variable is a column, each observation is a row, and each type of observational unit is a table". This allows a standard data structure for which data analysis tools can be consistently built around. Importance: Cited over 1,500 times, this effort for tidy data has been described by David Donoho as having "more impact on today's practice of data analysis than many highly regarded theoretical statistics articles". In the context of data visualization, this publication is said to support "efficient exploration and prototyping because variables can be assigned different roles in the plot without modifying anything about the original dataset". Data Organization in Spreadsheets Author: Karl W. Broman and Kara H. Woo Publication data: Online version: https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375989 Description: This article offers practical recommendations for organizing data in spreadsheets, like Microsoft Excel and Google Sheets, to reduce errors and lower the barrier for later analyses due to limitations in spreadsheets or quirks in the software. Importance: Influences teaching both data and non-data practitioners to create more analysis-friendly spreadsheets, and has been described to outline "spreadsheet best practices". == Data visualizations == Quantitative Graphics in Statistics: A Brief History Author: James R. Beniger and Dorothy L. Robyn Publication data: Online version: https://www.jstor.org/stable/2683467 Description: Outlines history and evolution of quantitative graphics in statistics, going through spatial organization (17th and 18th centuries), discrete comparison (18th and 19th centuries), continuous distribution (19th century), and multivariate distribution and correlation (late 19th and 20th centuries). Importance: Helps put into perspective for learning data practitioners the recency of graphics that are used. A later publication "Graphical Methods in Statistics" by Stephen Fienberg in 1979 writes that his publication "owes much to the work of Beniger and Robyn". == Practice == Data Science for Business Author: Foster Provost and Tom Fawcett Publication data: Online version: N/A Description: Broadly outlines principles of data science and data-analytic thinking for businesses. Importance: Cited over 3,000 times, it is "highly recommended for students" but also it is also recommended due to its "relevance to senior management leaders who want to build and lead a team of data scientists and implement data science in solving complex business problems". == Tooling == Hidden Technical Debt in Machine Learning Systems Author: D. Sculley, Gary Holy, Daniel Golovin, Eugene Davydov, Todd Phillips, Dietmar Ebner, Vinay Chaudhary, Michael Young, Jean-François Crespo, Dan Dennison Publication data: Online version: https://proceedings.neurips.cc/paper_files/paper/2015/file/86df7dcfd896fcaf2674f757a2463eba-Paper.pdf Description: This paper argues that it is "dangerous to think of [complex machine learning] quick wins as coming for free" and overviews risk factors to account for when implementing a machine learning system. Importance: All authors worked for Google, article is cited over 2,000 times, and helped practitioners thinking about quickly implementing a machine learning tool without understanding the long-term maintenance of the tool. A few useful things to know about machine learning Author: Pedro Domingos Publication data: Online version: https://dl.acm.org/doi/10.1145/2347736.2347755 https://homes.cs.washington.edu/~pedrod/papers/cacm12.pdf Description: The purpose of this paper is to distill inaccessible "folk knowledge" to effectively implement machine learning projects because "machin

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  Computational learning theory

  In computer science, computational learning theory (or just learning theory) is a subfield of artificial intelligence devoted to studying the design and analysis of machine learning algorithms. == Overview == Theoretical results in machine learning often focus on a type of inductive learning known as supervised learning. In supervised learning, an algorithm is provided with labeled samples. For instance, the samples might be descriptions of mushrooms, with labels indicating whether they are edible or not. The algorithm uses these labeled samples to create a classifier. This classifier assigns labels to new samples, including those it has not previously encountered. The goal of the supervised learning algorithm is to optimize performance metrics, such as minimizing errors on new samples. In addition to performance bounds, computational learning theory studies the time complexity and feasibility of learning . In computational learning theory, a computation is considered feasible if it can be done in polynomial time . There are two kinds of time complexity results: Positive results – Showing that a certain class of functions is learnable in polynomial time. Negative results – Showing that certain classes cannot be learned in polynomial time. Negative results often rely on commonly believed, but yet unproven assumptions, such as: Computational complexity – P ≠ NP (the P versus NP problem); Cryptographic – One-way functions exist. There are several different approaches to computational learning theory based on making different assumptions about the inference principles used to generalise from limited data. This includes different definitions of probability (see frequency probability, Bayesian probability) and different assumptions on the generation of samples. The different approaches include: Exact learning, proposed by Dana Angluin; Probably approximately correct learning (PAC learning), proposed by Leslie Valiant; VC theory, proposed by Vladimir Vapnik and Alexey Chervonenkis; Inductive inference as developed by Ray Solomonoff; Algorithmic learning theory, from the work of E. Mark Gold; Online machine learning, from the work of Nick Littlestone. While its primary goal is to understand learning abstractly, computational learning theory has led to the development of practical algorithms. For example, PAC theory inspired boosting, VC theory led to support vector machines, and Bayesian inference led to belief networks.

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  Blockmodeling

  Blockmodeling is a set or a coherent framework, that is used for analyzing social structure and also for setting procedure(s) for partitioning (clustering) social network's units (nodes, vertices, actors), based on specific patterns, which form a distinctive structure through interconnectivity. It is primarily used in statistics, machine learning and network science. As an empirical procedure, blockmodeling assumes that all the units in a specific network can be grouped together to such extent to which they are equivalent. Regarding equivalency, it can be structural, regular or generalized. Using blockmodeling, a network can be analyzed using newly created blockmodels, which transforms large and complex network into a smaller and more comprehensible one. At the same time, the blockmodeling is used to operationalize social roles. While some contend that the blockmodeling is just clustering methods, Bonacich and McConaghy state that "it is a theoretically grounded and algebraic approach to the analysis of the structure of relations". Blockmodeling's unique ability lies in the fact that it considers the structure not just as a set of direct relations, but also takes into account all other possible compound relations that are based on the direct ones. The principles of blockmodeling were first introduced by Francois Lorrain and Harrison C. White in 1971. Blockmodeling is considered as "an important set of network analytic tools" as it deals with delineation of role structures (the well-defined places in social structures, also known as positions) and the discerning the fundamental structure of social networks. According to Batagelj, the primary "goal of blockmodeling is to reduce a large, potentially incoherent network to a smaller comprehensible structure that can be interpreted more readily". Blockmodeling was at first used for analysis in sociometry and psychometrics, but has now spread also to other sciences. == Definition == A network as a system is composed of (or defined by) two different sets: one set of units (nodes, vertices, actors) and one set of links between the units. Using both sets, it is possible to create a graph, describing the structure of the network. During blockmodeling, the researcher is faced with two problems: how to partition the units (e.g., how to determine the clusters (or classes), that then form vertices in a blockmodel) and then how to determine the links in the blockmodel (and at the same time the values of these links). In the social sciences, the networks are usually social networks, composed of several individuals (units) and selected social relationships among them (links). Real-world networks can be large and complex; blockmodeling is used to simplify them into smaller structures that can be easier to interpret. Specifically, blockmodeling partitions the units into clusters and then determines the ties among the clusters. At the same time, blockmodeling can be used to explain the social roles existing in the network, as it is assumed that the created cluster of units mimics (or is closely associated with) the units' social roles. Blockmodeling can thus be defined as a set of approaches for partitioning units into clusters (also known as positions) and links into blocks, which are further defined by the newly obtained clusters. A block (also blockmodel) is defined as a submatrix, that shows interconnectivity (links) between nodes, present in the same or different clusters. Each of these positions in the cluster is defined by a set of (in)direct ties to and from other social positions. These links (connections) can be directed or undirected; there can be multiple links between the same pair of objects or they can have weights on them. If there are not any multiple links in a network, it is called a simple network. A matrix representation of a graph is composed of ordered units, in rows and columns, based on their names. The ordered units with similar patterns of links are partitioned together in the same clusters. Clusters are then arranged together so that units from the same clusters are placed next to each other, thus preserving interconnectivity. In the next step, the units (from the same clusters) are transformed into a blockmodel. With this, several blockmodels are usually formed, one being core cluster and others being cohesive; a core cluster is always connected to cohesive ones, while cohesive ones cannot be linked together. Clustering of nodes is based on the equivalence, such as structural and regular. The primary objective of the matrix form is to visually present relations between the persons included in the cluster. These ties are coded dichotomously (as present or absent), and the rows in the matrix form indicate the source of the ties, while the columns represent the destination of the ties. Equivalence can have two basic approaches: the equivalent units have the same connection pattern to the same neighbors or these units have same or similar connection pattern to different neighbors. If the units are connected to the rest of network in identical ways, then they are structurally equivalent. Units can also be regularly equivalent, when they are equivalently connected to equivalent others. With blockmodeling, it is necessary to consider the issue of results being affected by measurement errors in the initial stage of acquiring the data. == Different approaches == Regarding what kind of network is undergoing blockmodeling, a different approach is necessary. Networks can be one–mode or two–mode. In the former all units can be connected to any other unit and where units are of the same type, while in the latter the units are connected only to the unit(s) of a different type. Regarding relationships between units, they can be single–relational or multi–relational networks. Further more, the networks can be temporal or multilevel and also binary (only 0 and 1) or signed (allowing negative ties)/values (other values are possible) networks. Different approaches to blockmodeling can be grouped into two main classes: deterministic blockmodeling and stochastic blockmodeling approaches. Deterministic blockmodeling is then further divided into direct and indirect blockmodeling approaches. Among direct blockmodeling approaches are: structural equivalence and regular equivalence. Structural equivalence is a state, when units are connected to the rest of the network in an identical way(s), while regular equivalence occurs when units are equally related to equivalent others (units are not necessarily sharing neighbors, but have neighbour that are themselves similar). Indirect blockmodeling approaches, where partitioning is dealt with as a traditional cluster analysis problem (measuring (dis)similarity results in a (dis)similarity matrix), are: conventional blockmodeling, generalized blockmodeling: generalized blockmodeling of binary networks, generalized blockmodeling of valued networks and generalized homogeneity blockmodeling, prespecified blockmodeling. According to Brusco and Steinley (2011), the blockmodeling can be categorized (using a number of dimensions): deterministic or stochastic blockmodeling, one–mode or two–mode networks, signed or unsigned networks, exploratory or confirmatory blockmodeling. == Blockmodels == Blockmodels (sometimes also block models) are structures in which: vertices (e.g., units, nodes) are assembled within a cluster, with each cluster identified as a vertex; from such vertices a graph can be constructed; combinations of all the links (ties), represented in a block as a single link between positions, while at the same time constructing one tie for each block. In a case, when there are no ties in a block, there will be no ties between the two positions that define the block. Computer programs can partition the social network according to pre-set conditions. When empirical blocks can be reasonably approximated in terms of ideal blocks, such blockmodels can be reduced to a blockimage, which is a representation of the original network, capturing its underlying 'functional anatomy'. Thus, blockmodels can "permit the data to characterize their own structure", and at the same time not seek to manifest a preconceived structure imposed by the researcher. Blockmodels can be created indirectly or directly, based on the construction of the criterion function. Indirect construction refers to a function, based on "compatible (dis)similarity measure between paris of units", while the direct construction is "a function measuring the fit of real blocks induced by a given clustering to the corresponding ideal blocks with perfect relations within each cluster and between clusters according to the considered types of connections (equivalence)". === Types === Blockmodels can be specified regarding the intuition, substance or the insight into the nature of the studied network; this can result in such models as follows: parent-child role systems, organizational hierarchies, systems of

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  Physical neural network

  A physical neural network is a type of artificial neural network in which an electrically adjustable material is used to emulate the function of a neural synapse or a higher-order (dendritic) neuron model. "Physical" neural network is used to emphasize the reliance on physical hardware used to emulate neurons as opposed to software-based approaches. More generally the term is applicable to other artificial neural networks in which a memristor or other electrically adjustable resistance material is used to emulate a neural synapse. == Types of physical neural networks == === ADALINE === In the 1960s Bernard Widrow and Ted Hoff developed ADALINE (Adaptive Linear Neuron) which used electrochemical cells called memistors (memory resistors) to emulate synapses of an artificial neuron. The memistors were implemented as 3-terminal devices operating based on the reversible electroplating of copper such that the resistance between two of the terminals is controlled by the integral of the current applied via the third terminal. The ADALINE circuitry was briefly commercialized by the Memistor Corporation in the 1960s enabling some applications in pattern recognition. However, since the memistors were not fabricated using integrated circuit fabrication techniques the technology was not scalable and was eventually abandoned as solid-state electronics became mature. === Analog VLSI === In 1989 Carver Mead published his book Analog VLSI and Neural Systems, which spun off perhaps the most common variant of analog neural networks. The physical realization is implemented in analog VLSI. This is often implemented as field effect transistors in low inversion. Such devices can be modelled as translinear circuits. This is a technique described by Barrie Gilbert in several papers around mid 1970th, and in particular his Translinear Circuits from 1981. With this method circuits can be analyzed as a set of well-defined functions in steady-state, and such circuits assembled into complex networks. === Physical Neural Network === Alex Nugent describes a physical neural network as one or more nonlinear neuron-like nodes used to sum signals and nanoconnections formed from nanoparticles, nanowires, or nanotubes which determine the signal strength input to the nodes. Alignment or self-assembly of the nanoconnections is determined by the history of the applied electric field performing a function analogous to neural synapses. Numerous applications for such physical neural networks are possible. For example, a temporal summation device can be composed of one or more nanoconnections having an input and an output thereof, wherein an input signal provided to the input causes one or more of the nanoconnection to experience an increase in connection strength thereof over time. Another example of a physical neural network is taught by U.S. Patent No. 7,039,619 entitled "Utilized nanotechnology apparatus using a neural network, a solution and a connection gap," which issued to Alex Nugent by the U.S. Patent & Trademark Office on May 2, 2006. A further application of physical neural network is shown in U.S. Patent No. 7,412,428 entitled "Application of hebbian and anti-hebbian learning to nanotechnology-based physical neural networks," which issued on August 12, 2008. Nugent and Molter have shown that universal computing and general-purpose machine learning are possible from operations available through simple memristive circuits operating the AHaH plasticity rule. More recently, it has been argued that also complex networks of purely memristive circuits can serve as neural networks. === Phase change neural network === In 2002, Stanford Ovshinsky described an analog neural computing medium in which phase-change material has the ability to cumulatively respond to multiple input signals. An electrical alteration of the resistance of the phase change material is used to control the weighting of the input signals. === Memristive neural network === Greg Snider of HP Labs describes a system of cortical computing with memristive nanodevices. The memristors (memory resistors) are implemented by thin film materials in which the resistance is electrically tuned via the transport of ions or oxygen vacancies within the film. DARPA's SyNAPSE project has funded IBM Research and HP Labs, in collaboration with the Boston University Department of Cognitive and Neural Systems (CNS), to develop neuromorphic architectures which may be based on memristive systems. === Protonic artificial synapses === In 2022, researchers reported the development of nanoscale brain-inspired artificial synapses, using the ion proton (H+), for 'analog deep learning'.

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  AI literacy

  AI literacy or artificial intelligence literacy is "a set of competencies that enables individuals to critically evaluate AI technologies; communicate and collaborate effectively with AI; and use AI as a tool online, at home, and in the workplace." AI is employed in a variety of applications, including self-driving automobiles, virtual assistants and text generation by generative AI models. Users of these tools should be able to make informed decisions. AI literacy may have an impact on students' future employment prospects. With the rise of generative AI platforms, AI literacy has become a topic of conversation in the field of education. Some think AI literacy is essential for school and college students, while others restrict or prohibit the use of AI in assignments, viewing it as a form of academic dishonesty. However, many researchers and educational institutions promote a more nuanced approach, encouraging critical engagement with AI while developing policies that balance academic integrity with opportunities for learning. == Definitions == Other definitions of AI literacy include the ability to understand, use, monitor, and critically reflect on AI applications. That use of the term usually refers to teaching skills and knowledge to the general public, particularly those who are not adept in AI and the ability to understand, use, evaluate, and ethically navigate AI. As research into AI literacy is still emerging and focused on developing context-specific skills, there is not yet a single, broadly agreed-upon definition. AI literacy is linked to other forms of literacy. AI literacy requires digital literacy, whereas scientific and computational literacy may inform it. Data literacy also significantly overlaps with it. == Categories == AI literacy encompasses multiple categories, including a theoretical understanding of how artificial intelligence works, the usage of artificial intelligence technologies, and the critical appraisal of artificial intelligence, and its ethics. === Know and understand AI === Knowledge and understanding of AI refers to a basic understanding of what artificial intelligence is and how it works. This includes familiarity with machine learning algorithms and the limitations and biases present in AI systems. Users who know and understand AI should be familiar with various technologies that use artificial intelligence, including cognitive systems, robotics and machine learning. This includes recognizing that large language models (LLMs) are machine learning models trained on extensive datasets which generate new text rather than retrieving pre-written responses. === Use and apply AI === Using and applying AI refers to the ability to use AI tools to solve problems and perform tasks such as programming and analyzing big data. Some consider prompt engineering, the practice of designing effective prompts to guide generative AI platforms more effectively, as another competency within AI literacy. === Evaluate and create AI === Evaluation and creation refers to the ability to critically evaluate the quality and reliability of AI systems. It also refers to designing and building fair and ethical AI systems. To evaluate correctly, users should also learn in which areas AI is strong, and in which areas it is weak. === AI ethics === AI ethics refers to understanding the moral implications of AI, and the making informed decisions regarding the use of AI tools. This area includes considerations such as: Accountability: Hold AI actors accountable for the operation of AI systems and adherence to ethical ideals. Accuracy: Identify and report sources of error and uncertainty in algorithms and data. Auditability: Enable other parties to audit and assess algorithm behavior via transparent information sharing. Explainability: Make sure that algorithmic judgments and the underlying data can be presented in simple language. Fairness: Prevent biases and consider varied viewpoints. To do so, increase the diversity of researchers in the field. Human Centricity and Well-being: Prioritize human well-being in AI development and deployment. Human rights Alignment: Ensure that technology do not infringe internationally recognized human rights. Inclusivity: Make AI accessible to everyone. Progress: Choose high value initiatives. Responsibility, accountability, and transparency: Foster trust via responsibility, accountability, and fairness. Robustness and Security: Make AI systems safe, secure, and resistant to manipulation or data breach. Sustainability: Choose implementations that generate long-term, useful benefits. Environmental Implications: How this tool impacts the environment, any restrictions or laws, if this impact is worth the effects or not. === Enabling AI === Support AI by developing associated knowledge and skills such as programming and statistics. == Promoting AI literacy == Several governments have recognized the need to promote AI literacy, including among adults. Such programs have been published in the United States, China, Germany and Finland. Programs intended for the general public usually consist of short and easy to understand online study units. Programs intended for children are usually project-based. Programs for students at colleges and universities often address the specific professional needs of the student, depending on their field of study. Beyond the education system, AI literacy can also be developed in the community, for example in museums. === Schools === Schools use diverse pedagogies to promote AI literacy. These include: Performing a Turing test with an intelligent agent Creating chatbots Building apps using Blockly-based programming Project-based learning Building robots Data visualization Training AI models Artificial intelligence curricula can improve students' understanding of topics such as machine learning, neural networks, and deep learning. === Higher education === Before the second decade of the 21st century, artificial intelligence was studied mainly in STEM courses. Later, projects emerged to increase artificial intelligence education, specifically to promote AI literacy. Most courses start with one or more study units that deal with basic questions such as what artificial intelligence is, where it comes from, what it can do and what it can't do. Most courses also refer to machine learning and deep learning. Some of the courses deal with moral issues in artificial intelligence. In Ireland, the Higher Education Authority published Generative AI in Higher Education Teaching & Learning: Policy Framework in December 2025, which encouraged higher education institutions to embed AI literacy across programmes as a core graduate attribute. ==== Disciplinary policy ==== As a response to the increase of generative AI use in education, several disciplines formed committees or task forces to examine context-specific approaches toward AI literacy. In spring 2025, the Modern Language Association and Conference on College Composition and Communication Joint Task Force finished development of three working papers, a guide on AI literacy for students, and a collection of resources addressing AI use in writing. The task force emphasized the need for "a culture of critical AI literacy" and included guidelines not only for students but also educators and institutions, highlighting the need for modeling ethical AI use in planning processes. Similarly, a committee formed by the American Historical Association Council published "Guiding Principles for Artificial Intelligence in History Education" which encouraged "clear and transparent engagement with generative AI." The guidelines demonstrate the value of criticality when working with generative AI in thinking and research.

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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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  Silhouette (clustering)

  Silhouette is a method of interpretation and validation of consistency within clusters of data. The technique provides a succinct graphical representation of how well each object has been classified. It was proposed by Belgian statistician Peter Rousseeuw in 1987. The silhouette value is a measure of how similar an object is to its own cluster (cohesion) compared to other clusters (separation). The silhouette value ranges from −1 to +1, where a high value indicates that the object is well matched to its own cluster and poorly matched to neighboring clusters. If most objects have a high value, then the clustering configuration is appropriate. If many points have a low or negative value, then the clustering configuration may have too many or too few clusters. A clustering with an average silhouette width of over 0.7 is considered to be "strong", a value over 0.5 "reasonable", and over 0.25 "weak". However, with an increasing dimensionality of the data, it becomes difficult to achieve such high values because of the curse of dimensionality, as the distances become more similar. The silhouette score is specialized for measuring cluster quality when the clusters are convex-shaped, and may not perform well if the data clusters have irregular shapes or are of varying sizes. The silhouette value can be calculated with any distance metric, such as Euclidean distance or Manhattan distance. == Definition == Assume the data have been clustered via any technique, such as k-medoids or k-means, into k {\displaystyle k} clusters. For data point i ∈ C i {\displaystyle i\in C_{i}} (data point i {\displaystyle i} in the cluster C i {\displaystyle C_{i}} ), calculate a ( i ) {\displaystyle a(i)} , the average distance that i {\displaystyle i} is from all other points in that cluster: a ( i ) = 1 | C i | − 1 ∑ j ∈ C i , i ≠ j d ( i , j ) {\displaystyle a(i)={\frac {1}{|C_{i}|-1}}\sum _{j\in C_{i},i\neq j}d(i,j)} where | C i | {\displaystyle |C_{i}|} is the number of points belonging to cluster C i {\displaystyle C_{i}} , and d ( i , j ) {\displaystyle d(i,j)} is the distance between data points i {\displaystyle i} and j {\displaystyle j} in the cluster C i {\displaystyle C_{i}} (we divide by | C i | − 1 {\displaystyle |C_{i}|-1} because the distance d ( i , i ) {\displaystyle d(i,i)} is not included in the sum). a ( i ) {\displaystyle a(i)} can be interpreted as a measure of how well i {\displaystyle i} is assigned to its cluster (the smaller the value, the better the assignment). We then define the mean dissimilarity of point i {\displaystyle i} to some cluster C j {\displaystyle C_{j}} as the mean of the distance from i {\displaystyle i} to all points in C j {\displaystyle C_{j}} (where C j ≠ C i {\displaystyle C_{j}\neq C_{i}} ). For each data point i ∈ C i {\displaystyle i\in C_{i}} , we now define b ( i ) {\displaystyle b(i)} as the average distance between i {\displaystyle i} and the points in the closest cluster (hence: "min") that i {\displaystyle i} does not belong to: b ( i ) = min j ≠ i 1 | C j | ∑ l ∈ C j d ( i , l ) {\displaystyle b(i)=\min _{j\neq i}{\frac {1}{|C_{j}|}}\sum _{l\in C_{j}}d(i,l)} The cluster with the smallest mean dissimilarity is said to be the "neighboring cluster" of i {\displaystyle i} because it is the next best fit cluster for point i {\displaystyle i} . We now define a silhouette (value) of one data point i {\displaystyle i} s ( i ) = b ( i ) − a ( i ) max { a ( i ) , b ( i ) } {\displaystyle s(i)={\frac {b(i)-a(i)}{\max\{a(i),b(i)\}}}} , if | C i | > 1 {\displaystyle |C_{i}|>1} and s ( i ) = 0 {\displaystyle s(i)=0} , if | C i | = 1 {\displaystyle |C_{i}|=1} , which can also be written as s ( i ) = { 1 − a ( i ) b ( i ) , if a ( i ) < b ( i ) 0 , if a ( i ) = b ( i ) b ( i ) a ( i ) − 1 , if a ( i ) > b ( i ) {\displaystyle s(i)={\begin{cases}1-{\frac {a(i)}{b(i)}},&{\mbox{ if }}a(i)b(i)\\\end{cases}}} From the above definition, s ( i ) {\displaystyle s(i)} is bounded to the interval [ − 1 , 1 ] {\displaystyle [-1,1]} , i.e. − 1 ≤ s ( i ) ≤ 1. {\displaystyle -1\leq s(i)\leq 1.} Note that a ( i ) {\displaystyle a(i)} is not clearly defined for clusters with size = 1, in which case we set s ( i ) = 0 {\displaystyle s(i)=0} . This choice is arbitrary, but neutral in the sense that it is at the midpoint of the bounds, -1 and 1. For s ( i ) {\displaystyle s(i)} to be close to 1 we require a ( i ) ≪ b ( i ) {\displaystyle a(i)\ll b(i)} . As a ( i ) {\displaystyle a(i)} is a measure of how dissimilar i {\displaystyle i} is to its own cluster, a small value means it is well matched. Furthermore, a large b ( i ) {\displaystyle b(i)} implies that i {\displaystyle i} is badly matched to its neighbouring cluster. Thus an s ( i ) {\displaystyle s(i)} close to 1 means that the data is appropriately clustered. If s ( i ) {\displaystyle s(i)} is close to -1, then by the same logic we see that i {\displaystyle i} would be more appropriate if it was clustered in its neighbouring cluster. An s ( i ) {\displaystyle s(i)} near zero means that the datum is on the border of two natural clusters. The mean s ( i ) {\displaystyle s(i)} over all points of a cluster is a measure of how tightly grouped all the points in the cluster are. Thus the mean s ( i ) {\displaystyle s(i)} over all data of the entire dataset is a measure of how appropriately the data have been clustered. If there are too many or too few clusters, as may occur when a poor choice of k {\displaystyle k} is used in the clustering algorithm (e.g., k-means), some of the clusters will typically display much narrower silhouettes than the rest. Thus silhouette plots and means may be used to determine the natural number of clusters within a dataset. One can also increase the likelihood of the silhouette being maximized at the correct number of clusters by re-scaling the data using feature weights that are cluster specific. Kaufman et al. introduced the term silhouette coefficient for the maximum value of the mean s ( i ) {\displaystyle s(i)} over all data of the entire dataset, i.e., S C = max k s ~ ( k ) , {\displaystyle SC=\max _{k}{\tilde {s}}\left(k\right),} where s ~ ( k ) {\displaystyle {\tilde {s}}\left(k\right)} represents the mean s ( i ) {\displaystyle s(i)} over all data of the entire dataset for a specific number of clusters k {\displaystyle k} . The silhouette coefficient describes the best possible clustering possible for a given number of clusters, as measured by the highest average silhouette score for all points in the dataset. == Simplified and medoid silhouette == Computing the silhouette coefficient needs all O ( N 2 ) {\displaystyle {\mathcal {O}}(N^{2})} pairwise distances, making this evaluation much more costly than clustering with k-means. For a clustering with centers μ C I {\displaystyle \mu _{C_{I}}} for each cluster C I {\displaystyle C_{I}} , we can use the following simplified Silhouette for each point i ∈ C I {\displaystyle i\in C_{I}} instead, which can be computed using only O ( N k ) {\displaystyle {\mathcal {O}}(Nk)} distances: a ′ ( i ) = d ( i , μ C I ) {\displaystyle a'(i)=d(i,\mu _{C_{I}})} and b ′ ( i ) = min C J ≠ C I d ( i , μ C J ) {\displaystyle b'(i)=\min _{C_{J}\neq C_{I}}d(i,\mu _{C_{J}})} , which has the additional benefit that a ′ ( i ) {\displaystyle a'(i)} is always defined, then define accordingly the simplified silhouette and simplified silhouette coefficient s ′ ( i ) = b ′ ( i ) − a ′ ( i ) max { a ′ ( i ) , b ′ ( i ) } {\displaystyle s'(i)={\frac {b'(i)-a'(i)}{\max\{a'(i),b'(i)\}}}} S C ′ = max k 1 N ∑ i s ′ ( i ) {\displaystyle SC'=\max _{k}{\frac {1}{N}}\sum _{i}s'\left(i\right)} . If the cluster centers are medoids (as in k-medoids clustering) instead of arithmetic means (as in k-means clustering), this is also called the medoid-based silhouette or medoid silhouette. If every object is assigned to the nearest medoid (as in k-medoids clustering), we know that a ′ ( i ) ≤ b ′ ( i ) {\displaystyle a'(i)\leq b'(i)} , and hence s ′ ( i ) = b ′ ( i ) − a ′ ( i ) b ′ ( i ) = 1 − a ′ ( i ) b ′ ( i ) {\displaystyle s'(i)={\frac {b'(i)-a'(i)}{b'(i)}}=1-{\frac {a'(i)}{b'(i)}}} . == Silhouette clustering == Instead of using the average silhouette to evaluate a clustering obtained from, e.g., k-medoids or k-means, we can try to directly find a solution that maximizes the Silhouette. We do not have a closed form solution to maximize this, but it will usually be best to assign points to the nearest cluster as done by these methods. Van der Laan et al. proposed to adapt the standard algorithm for k-medoids, PAM, for this purpose and call this algorithm PAMSIL: Choose initial medoids by using PAM Compute the average silhouette of this initial solution For each pair of a medoid m and a non-medoid x swap m and x compute the average silhouette of the resulting solution remember the best swap un-swap m and x for the next iteration Perform the best swap and return to

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  Variable kernel density estimation

  In statistics, adaptive or "variable-bandwidth" kernel density estimation is a form of kernel density estimation in which the size of the kernels used in the estimate are varied depending upon either the location of the samples or the location of the test point. It is a particularly effective technique when the sample space is multi-dimensional. == Rationale == Given a set of samples, { x → i } {\displaystyle \lbrace {\vec {x}}_{i}\rbrace } , we wish to estimate the density, P ( x → ) {\displaystyle P({\vec {x}})} , at a test point, x → {\displaystyle {\vec {x}}} : P ( x → ) ≈ W n h D {\displaystyle P({\vec {x}})\approx {\frac {W}{nh^{D}}}} W = ∑ i = 1 n w i {\displaystyle W=\sum _{i=1}^{n}w_{i}} w i = K ( x → − x → i h ) {\displaystyle w_{i}=K\left({\frac {{\vec {x}}-{\vec {x}}_{i}}{h}}\right)} where n is the number of samples, K is the "kernel", h is its width and D is the number of dimensions in x → {\displaystyle {\vec {x}}} . The kernel can be thought of as a simple, linear filter. Using a fixed filter width may mean that in regions of low density, all samples will fall in the tails of the filter with very low weighting, while regions of high density will find an excessive number of samples in the central region with weighting close to unity. To fix this problem, we vary the width of the kernel in different regions of the sample space. There are two methods of doing this: balloon and pointwise estimation. In a balloon estimator, the kernel width is varied depending on the location of the test point. In a pointwise estimator, the kernel width is varied depending on the location of the sample. For multivariate estimators, the parameter, h, can be generalized to vary not just the size, but also the shape of the kernel. This more complicated approach will not be covered here. == Balloon estimators == A common method of varying the kernel width is to make it inversely proportional to the density at the test point: h = k [ n P ( x → ) ] 1 / D {\displaystyle h={\frac {k}{\left[nP({\vec {x}})\right]^{1/D}}}} where k is a constant. If we back-substitute the estimated PDF, and assuming a Gaussian kernel function, we can show that W is a constant: W = k D ( 2 π ) D / 2 {\displaystyle W=k^{D}(2\pi )^{D/2}} A similar derivation holds for any kernel whose normalising function is of the order hD, although with a different constant factor in place of the (2 π)D/2 term. This produces a generalization of the k-nearest neighbour algorithm. That is, a uniform kernel function will return the KNN technique. There are two components to the error: a variance term and a bias term. The variance term is given as: e 1 = P ∫ K 2 n h D {\displaystyle e_{1}={\frac {P\int K^{2}}{nh^{D}}}} . The bias term is found by evaluating the approximated function in the limit as the kernel width becomes much larger than the sample spacing. By using a Taylor expansion for the real function, the bias term drops out: e 2 = h 2 n ∇ 2 P {\displaystyle e_{2}={\frac {h^{2}}{n}}\nabla ^{2}P} An optimal kernel width that minimizes the error of each estimate can thus be derived. == Use for statistical classification == The method is particularly effective when applied to statistical classification. There are two ways we can proceed: the first is to compute the PDFs of each class separately, using different bandwidth parameters, and then compare them as in Taylor. Alternatively, we can divide up the sum based on the class of each sample: P ( j , x → ) ≈ 1 n ∑ i = 1 , c i = j n w i {\displaystyle P(j,{\vec {x}})\approx {\frac {1}{n}}\sum _{i=1,c_{i}=j}^{n}w_{i}} where ci is the class of the ith sample. The class of the test point may be estimated through maximum likelihood.

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  Mooky (app)

  Mooky was a location-based social and dating application, designed to help its users to find the perfect match by providing a large scale of filters. Mooky was free of charge. The app made use of mobile devices' geolocation, a feature of smart phones and other devices which allows users to locate other users who are nearby. == History == Mooky was published on Google Play on April 17, 2016, by Mooky BV. The latest version of this application was version 1.0.6. == Overview == === How it works === Mooky used Facebook to build a user profile with photos and basic information, like the user's surname and age. From there on the user had to fill in their Mooky profile, which contains information about the user's height, posture, hair color, eye color, ethnicity and religion. After this the user could select its preferences to find matches nearby. === User verification === Mooky asked their users to take a selfie holding a piece of paper saying 'Mooky'. Mooky would then manually accept or decline the user verification.

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  Markov blanket

  In statistics and machine learning, a Markov blanket of a random variable is a set of variables that renders the variable conditionally independent of all other variables in the system. This concept is central in probabilistic graphical models and feature selection. If a Markov blanket is minimal—meaning that no variable in it can be removed without losing this conditional independence—it is called a Markov boundary. Identifying a Markov blanket or boundary allows for efficient inference and helps isolate relevant variables for prediction or causal reasoning. The terms Markov blanket and Markov boundary were coined by Judea Pearl in 1988. A Markov blanket may be derived from the structure of a probabilistic graphical model such as a Bayesian network or Markov random field. == Definition == A Markov blanket of a random variable Y {\displaystyle Y} in a random variable set S = { X 1 , … , X n } {\displaystyle {\mathcal {S}}=\{X_{1},\ldots ,X_{n}\}} is any subset S 1 {\displaystyle {\mathcal {S}}_{1}} of S {\displaystyle {\mathcal {S}}} , conditioned on which other variables are independent with Y {\displaystyle Y} : Y ⊥ ⊥ S ∖ S 1 ∣ S 1 {\displaystyle Y\perp \!\!\!\perp {\mathcal {S}}\smallsetminus {\mathcal {S}}_{1}\mid {\mathcal {S}}_{1}} It means that S 1 {\displaystyle {\mathcal {S}}_{1}} contains at least all the information one needs to infer Y {\displaystyle Y} , where the variables in S ∖ S 1 {\displaystyle {\mathcal {S}}\smallsetminus {\mathcal {S}}_{1}} are redundant. In general, a given Markov blanket is not unique. Any set in S {\displaystyle {\mathcal {S}}} that contains a Markov blanket is also a Markov blanket itself. Specifically, S {\displaystyle {\mathcal {S}}} is a Markov blanket of Y {\displaystyle Y} in S {\displaystyle {\mathcal {S}}} . === Example === In a Bayesian network, the Markov blanket of a node consists of its parents, its children, and its children's other parents (i.e., co-parents). Knowing the values of these nodes makes the target node conditionally independent of the rest of the network. In a Markov random field, the Markov blanket of a node is simply its immediate neighbors. == Markov condition == The concept of a Markov blanket is rooted in the Markov condition, which states that in a probabilistic graphical model, each variable is conditionally independent of its non-descendants given its parents. This condition implies the existence of a minimal separating set — the Markov blanket — that shields a variable from the rest of the network. For instance, when a person holds an object stationary against gravity, the object’s acceleration is fully determined by its direct causes—namely, the upward force from the hand and the downward gravitational pull. Other variables such as air pressure or temperature are causally irrelevant. == Markov boundary == A Markov boundary of Y {\displaystyle Y} in S {\displaystyle {\mathcal {S}}} is a subset S 2 {\displaystyle {\mathcal {S}}_{2}} of S {\displaystyle {\mathcal {S}}} , such that S 2 {\displaystyle {\mathcal {S}}_{2}} itself is a Markov blanket of Y {\displaystyle Y} , but any proper subset of S 2 {\displaystyle {\mathcal {S}}_{2}} is not a Markov blanket of Y {\displaystyle Y} . In other words, a Markov boundary is a minimal Markov blanket. The Markov boundary of a node A {\displaystyle A} in a Bayesian network is the set of nodes composed of A {\displaystyle A} 's parents, A {\displaystyle A} 's children, and A {\displaystyle A} 's children's other parents. In a Markov random field, the Markov boundary for a node is the set of its neighboring nodes. In a dependency network, the Markov boundary for a node is the set of its parents. === Uniqueness of Markov boundary === The Markov boundary always exists. Under some mild conditions, the Markov boundary is unique. However, for most practical and theoretical scenarios multiple Markov boundaries may provide alternative solutions. When there are multiple Markov boundaries, quantities measuring causal effect could fail. == In cognitive science == In the study of consciousness, brain function, and complex adaptive systems, Markov blankets are proposed as a mathematical mechanism which delimits the extent of cognitive entities, whether it be physical or causal.

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  Clustering illusion

  The clustering illusion is the tendency to erroneously consider the inevitable "streaks" or "clusters" arising in small samples from random distributions to be non-random. The illusion is caused by a human tendency to underpredict the amount of variability likely to appear in a small sample of random or pseudorandom data. Thomas Gilovich, an early author on the subject, argued that the effect occurs for different types of random dispersions. Some might perceive patterns in stock market price fluctuations over time, or clusters in two-dimensional data such as the locations of impact of World War II V-1 flying bombs on maps of London. Although Londoners developed specific theories about the pattern of impacts within London, a statistical analysis by R. D. Clarke originally published in 1946 showed that the impacts of V-2 rockets on London were a close fit to a random distribution. == Similar biases == Using this cognitive bias in causal reasoning may result in the Texas sharpshooter fallacy, in which differences in data are ignored and similarities are overemphasized. More general forms of erroneous pattern recognition are pareidolia and apophenia. Related biases are the illusion of control which the clustering illusion could contribute to, and insensitivity to sample size in which people don't expect greater variation in smaller samples. A different cognitive bias involving misunderstanding of chance streams is the gambler's fallacy. == Possible causes == Daniel Kahneman and Amos Tversky explained this kind of misprediction as being caused by the representativeness heuristic (which itself they also first proposed).

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  Determining the number of clusters in a data set

  Determining the number of clusters in a data set, a quantity often labelled k as in the k-means algorithm, is a frequent problem in data clustering, and is a distinct issue from the process of actually solving the clustering problem. For a certain class of clustering algorithms (in particular k-means, k-medoids and expectation–maximization algorithm), there is a parameter commonly referred to as k that specifies the number of clusters to detect. Other algorithms such as DBSCAN and OPTICS algorithm do not require the specification of this parameter; hierarchical clustering avoids the problem altogether. The correct choice of k is often ambiguous, with interpretations depending on the shape and scale of the distribution of points in a data set and the desired clustering resolution of the user. In addition, increasing k without penalty will always reduce the amount of error in the resulting clustering, to the extreme case of zero error if each data point is considered its own cluster (i.e., when k equals the number of data points, n). Intuitively then, the optimal choice of k will strike a balance between maximum compression of the data using a single cluster, and maximum accuracy by assigning each data point to its own cluster. If an appropriate value of k is not apparent from prior knowledge of the properties of the data set, it must be chosen somehow. There are several categories of methods for making this decision. == Elbow method == The elbow method looks at the percentage of explained variance as a function of the number of clusters: One should choose a number of clusters so that adding another cluster does not give much better modeling of the data. More precisely, if one plots the percentage of variance explained by the clusters against the number of clusters, the first clusters will add much information (explain a lot of variance), but at some point the marginal gain will drop, giving an angle in the graph. The number of clusters is chosen at this point, hence the "elbow criterion". In most datasets, this "elbow" is ambiguous, making this method subjective and unreliable. Because the scale of the axes is arbitrary, the concept of an angle is not well-defined, and even on uniform random data, the curve produces an "elbow", making the method rather unreliable. Percentage of variance explained is the ratio of the between-group variance to the total variance, also known as an F-test. A slight variation of this method plots the curvature of the within group variance. The method can be traced to speculation by Robert L. Thorndike in 1953. While the idea of the elbow method sounds simple and straightforward, other methods (as detailed below) give better results. == X-means clustering == In statistics and data mining, X-means clustering is a variation of k-means clustering that refines cluster assignments by repeatedly attempting subdivision, and keeping the best resulting splits, until a criterion such as the Akaike information criterion (AIC) or Bayesian information criterion (BIC) is reached. == Information criterion approach == Another set of methods for determining the number of clusters are information criteria, such as the Akaike information criterion (AIC), Bayesian information criterion (BIC), or the deviance information criterion (DIC) — if it is possible to make a likelihood function for the clustering model. For example: The k-means model is "almost" a Gaussian mixture model and one can construct a likelihood for the Gaussian mixture model and thus also determine information criterion values. == Information–theoretic approach == Rate distortion theory has been applied to choosing k called the "jump" method, which determines the number of clusters that maximizes efficiency while minimizing error by information-theoretic standards. The strategy of the algorithm is to generate a distortion curve for the input data by running a standard clustering algorithm such as k-means for all values of k between 1 and n, and computing the distortion (described below) of the resulting clustering. The distortion curve is then transformed by a negative power chosen based on the dimensionality of the data. Jumps in the resulting values then signify reasonable choices for k, with the largest jump representing the best choice. The distortion of a clustering of some input data is formally defined as follows: Let the data set be modeled as a p-dimensional random variable, X, consisting of a mixture distribution of G components with common covariance, Γ. If we let c 1 … c K {\displaystyle c_{1}\ldots c_{K}} be a set of K cluster centers, with c X {\displaystyle c_{X}} the closest center to a given sample of X, then the minimum average distortion per dimension when fitting the K centers to the data is: d K = 1 p min c 1 … c K E [ ( X − c X ) T Γ − 1 ( X − c X ) ] {\displaystyle d_{K}={\frac {1}{p}}\min _{c_{1}\ldots c_{K}}{E[(X-c_{X})^{T}\Gamma ^{-1}(X-c_{X})]}} This is also the average Mahalanobis distance per dimension between X and the closest cluster center c X {\displaystyle c_{X}} . Because the minimization over all possible sets of cluster centers is prohibitively complex, the distortion is computed in practice by generating a set of cluster centers using a standard clustering algorithm and computing the distortion using the result. The pseudo-code for the jump method with an input set of p-dimensional data points X is: JumpMethod(X): Let Y = (p/2) Init a list D, of size n+1 Let D[0] = 0 For k = 1 ... n: Cluster X with k clusters (e.g., with k-means) Let d = Distortion of the resulting clustering D[k] = d^(-Y) Define J(i) = D[i] - D[i-1] Return the k between 1 and n that maximizes J(k) The choice of the transform power Y = ( p / 2 ) {\displaystyle Y=(p/2)} is motivated by asymptotic reasoning using results from rate distortion theory. Let the data X have a single, arbitrarily p-dimensional Gaussian distribution, and let fixed K = ⌊ α p ⌋ {\displaystyle K=\lfloor \alpha ^{p}\rfloor } , for some α greater than zero. Then the distortion of a clustering of K clusters in the limit as p goes to infinity is α − 2 {\displaystyle \alpha ^{-2}} . It can be seen that asymptotically, the distortion of a clustering to the power ( − p / 2 ) {\displaystyle (-p/2)} is proportional to α p {\displaystyle \alpha ^{p}} , which by definition is approximately the number of clusters K. In other words, for a single Gaussian distribution, increasing K beyond the true number of clusters, which should be one, causes a linear growth in distortion. This behavior is important in the general case of a mixture of multiple distribution components. Let X be a mixture of G p-dimensional Gaussian distributions with common covariance. Then for any fixed K less than G, the distortion of a clustering as p goes to infinity is infinite. Intuitively, this means that a clustering of less than the correct number of clusters is unable to describe asymptotically high-dimensional data, causing the distortion to increase without limit. If, as described above, K is made an increasing function of p, namely, K = ⌊ α p ⌋ {\displaystyle K=\lfloor \alpha ^{p}\rfloor } , the same result as above is achieved, with the value of the distortion in the limit as p goes to infinity being equal to α − 2 {\displaystyle \alpha ^{-2}} . Correspondingly, there is the same proportional relationship between the transformed distortion and the number of clusters, K. Putting the results above together, it can be seen that for sufficiently high values of p, the transformed distortion d K − p / 2 {\displaystyle d_{K}^{-p/2}} is approximately zero for K < G, then jumps suddenly and begins increasing linearly for K ≥ G. The jump algorithm for choosing K makes use of these behaviors to identify the most likely value for the true number of clusters. Although the mathematical support for the method is given in terms of asymptotic results, the algorithm has been empirically verified to work well in a variety of data sets with reasonable dimensionality. In addition to the localized jump method described above, there exists a second algorithm for choosing K using the same transformed distortion values known as the broken line method. The broken line method identifies the jump point in the graph of the transformed distortion by doing a simple least squares error line fit of two line segments, which in theory will fall along the x-axis for K < G, and along the linearly increasing phase of the transformed distortion plot for K ≥ G. The broken line method is more robust than the jump method in that its decision is global rather than local, but it also relies on the assumption of Gaussian mixture components, whereas the jump method is fully non-parametric and has been shown to be viable for general mixture distributions. == Silhouette method == The average silhouette of the data is another useful criterion for assessing the natural number of clusters. The silhouette of a data instance is a measure of how closely it is match

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  Security type system

  In computer science, a type system can be described as a syntactic framework which contains a set of rules that are used to assign a type property (int, boolean, char etc.) to various components of a computer program, such as variables or functions. A security type system works in a similar way, only with a main focus on the security of the computer program, through information flow control. Thus, the various components of the program are assigned security types, or labels. The aim of a such system is to ultimately be able to verify that a given program conforms to the type system rules and satisfies non-interference. Security type systems is one of many security techniques used in the field of language-based security, and is tightly connected to information flow and information flow policies. In simple terms, a security type system can be used to detect if there exists any kind of violation of confidentiality or integrity in a program, i.e. the programmer wants to detect if the program is in line with the information flow policy or not. == A simple information flow policy == Suppose there are two users, A and B. In a program, the following security classes (SC) are introduced: SC = {∅, {A}, {B}, {A,B}}, where ∅ is the empty set. The information flow policy should define the direction that information is allowed to flow, which is dependent on whether the policy allows read or write operations. This example considers read operations (confidentiality). The following flows are allowed: → = {({A}, {A}), ({B}, {B}), ({A,B}, {A,B}), ({A,B}, {A}), ({A,B}, {B}), ({A}, ∅), ({B}, ∅), ({A,B}, ∅)} This can also be described as a superset (⊇). In words: information is allowed to flow towards stricter levels of confidentiality. The combination operator (⊕) can express how security classes can perform read operations with respect to other security classes. For example: {A} ⊕ {A,B} = {A} — the only security class that can read from both {A} and {A,B} is {A}. {A} ⊕ {B} = ∅ — neither {A} nor {B} are allowed to read from both {A} and {B}. This can also be described as an intersection (∩) between security classes. An information flow policy can be illustrated as a Hasse diagram. The policy should also be a lattice, that is, it has a greatest lower-bound and least upper-bound (there always exists a combination between security classes). In the case of integrity, information will flow in the opposite direction, thus the policy will be inverted. == Information flow policy in security type systems == Once the policy is in place, the software developer can apply the security classes to the program components. Use of a security type system is usually combined with a compiler that can perform the verification of the information flow according to the type system rules. For the sake of simplicity, a very simple computer program, together with the information flow policy as described in the previous section, can be used as a demonstration. The simple program is given in the following pseudocode: if y{A} = 1 then x{A,B} := 0 else x{A,B} := 1 Here, an equality check is made on a variable y that is assigned the security class {A}. A variable x with a lower security class ({A,B}) is influenced by this check. This means that information is leaking from class {A} to class {A,B}, which is a violation of the confidentiality policy. This leak should be detected by the security type system. === Example === Designing a security type system requires a function (also known as a security environment) that creates a mapping from variables to security types, or classes. This function can be called Γ, such that Γ(x) = τ, where x is a variable and τ is the security class, or type. Security classes are assigned (also called "judgement") to program components, using the following notation: Types are assigned to read operations by: Γ ⊢ e : τ. Types are assigned to write operations by: Γ ⊢ S : τ cmd. Constants can be assigned any type. The following bottom-up notation can be used to decompose the program: ⁠assumption1 ... assumptionn/conclusion⁠. Once the program is decomposed into trivial judgements, by which the type can easily be determined, the types for the less trivial parts of the program can be derived. Each "numerator" is considered in isolation, looking at the type of each statement to see if an allowed type can be derived for the "denominator", based on the defined type system "rules". ==== Rules ==== The main part of the security type system is the rules. They say how the program should be decomposed and how type verification should be performed. This toy program consists of a conditional test and two possible variable assignments. Rules for these two events are defined as follows: Applying this to the simple program introduced above yields: The type system detects the policy violation in line 2, where a read operation of security class {A} is performed, followed by two write operations of a less strict security class {A,B}. In more formalized terms, {A} ⋢ {A,B}, {A,B} (from the rule of the conditional test). Thus, the program is classified as "not typeable". === Soundness === The soundness of a security type system can be informally defined as: If program P is well typed, P satisfies non-interference. Volpano, Smith and Irvine were the first to prove soundness of a security type system for a deterministic imperative programming language with a standard (non-instrumented) semantics using the notion of non-interference.

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  Curriculum learning

  Curriculum learning is a technique in machine learning in which a model is trained on examples of increasing difficulty, where the definition of "difficulty" may be provided externally or discovered as part of the training process. This is intended to attain good performance more quickly, or to converge to a better local optimum if the global optimum is not found. == Approach == Most generally, curriculum learning is the technique of successively increasing the difficulty of examples in the training set that is presented to a model over multiple training iterations. This can produce better results than exposing the model to the full training set immediately under some circumstances; most typically, when the model is able to learn general principles from easier examples, and then gradually incorporate more complex and nuanced information as harder examples are introduced, such as edge cases. This has been shown to work in many domains, most likely as a form of regularization. There are several major variations in how the technique is applied: A concept of "difficulty" must be defined. This may come from human annotation or an external heuristic; for example in language modeling, shorter sentences might be classified as easier than longer ones. Another approach is to use the performance of another model, with examples accurately predicted by that model being classified as easier (providing a connection to boosting). Difficulty can be increased steadily or in distinct epochs, and in a deterministic schedule or according to a probability distribution. This may also be moderated by a requirement for diversity at each stage, in cases where easier examples are likely to be disproportionately similar to each other. Applications must also decide the schedule for increasing the difficulty. Simple approaches may use a fixed schedule, such as training on easy examples for half of the available iterations and then all examples for the second half. Other approaches use self-paced learning to increase the difficulty in proportion to the performance of the model on the current set. Since curriculum learning only concerns the selection and ordering of training data, it can be combined with many other techniques in machine learning. The success of the method assumes that a model trained for an easier version of the problem can generalize to harder versions, so it can be seen as a form of transfer learning. Some authors also consider curriculum learning to include other forms of progressively increasing complexity, such as increasing the number of model parameters. It is frequently combined with reinforcement learning, such as learning a simplified version of a game first. Some domains have shown success with anti-curriculum learning: training on the most difficult examples first. One example is the ACCAN method for speech recognition, which trains on the examples with the lowest signal-to-noise ratio first. == History == The term "curriculum learning" was introduced by Yoshua Bengio et al in 2009, with reference to the psychological technique of shaping in animals and structured education for humans: beginning with the simplest concepts and then building on them. The authors also note that the application of this technique in machine learning has its roots in the early study of neural networks such as Jeffrey Elman's 1993 paper Learning and development in neural networks: the importance of starting small. Bengio et al showed good results for problems in image classification, such as identifying geometric shapes with progressively more complex forms, and language modeling, such as training with a gradually expanding vocabulary. They conclude that, for curriculum strategies, "their beneficial effect is most pronounced on the test set", suggesting good generalization. The technique has since been applied to many other domains: Natural language processing: Part-of-speech tagging Intent detection Sentiment analysis Machine translation Speech recognition Language model pre-training Image recognition: Facial recognition Object detection Reinforcement learning: Game-playing Graph learning Matrix factorization

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  Vapnik–Chervonenkis theory

  Vapnik–Chervonenkis theory (also known as VC theory) was developed during 1960–1990 by Vladimir Vapnik and Alexey Chervonenkis. The theory is a form of computational learning theory, which attempts to explain the learning process from a statistical point of view. == Introduction == VC theory covers at least four parts (as explained in The Nature of Statistical Learning Theory): Theory of consistency of learning processes What are (necessary and sufficient) conditions for consistency of a learning process based on the empirical risk minimization principle? Nonasymptotic theory of the rate of convergence of learning processes How fast is the rate of convergence of the learning process? Theory of controlling the generalization ability of learning processes How can one control the rate of convergence (the generalization ability) of the learning process? Theory of constructing learning machines How can one construct algorithms that can control the generalization ability? VC Theory is a major subbranch of statistical learning theory. One of its main applications in statistical learning theory is to provide generalization conditions for learning algorithms. From this point of view, VC theory is related to stability, which is an alternative approach for characterizing generalization. In addition, VC theory and VC dimension are instrumental in the theory of empirical processes, in the case of processes indexed by VC classes. Arguably these are the most important applications of the VC theory, and are employed in proving generalization. Several techniques will be introduced that are widely used in the empirical process and VC theory. The discussion is mainly based on the book Weak Convergence and Empirical Processes: With Applications to Statistics. == Overview of VC theory in empirical processes == === Background on empirical processes === Let ( X , A ) {\displaystyle ({\mathcal {X}},{\mathcal {A}})} be a measurable space. For any measure Q {\displaystyle Q} on ( X , A ) {\displaystyle ({\mathcal {X}},{\mathcal {A}})} , and any measurable functions f : X → R {\displaystyle f:{\mathcal {X}}\to \mathbf {R} } , define Q f = ∫ f d Q {\displaystyle Qf=\int fdQ} Measurability issues will be ignored here, for more technical detail see. Let F {\displaystyle {\mathcal {F}}} be a class of measurable functions f : X → R {\displaystyle f:{\mathcal {X}}\to \mathbf {R} } and define: ‖ Q ‖ F = sup { | Q f | : f ∈ F } . {\displaystyle \|Q\|_{\mathcal {F}}=\sup\{\vert Qf\vert \ :\ f\in {\mathcal {F}}\}.} Let X 1 , … , X n {\displaystyle X_{1},\ldots ,X_{n}} be independent, identically distributed random elements of ( X , A ) {\displaystyle ({\mathcal {X}},{\mathcal {A}})} . Then define the empirical measure P n = n − 1 ∑ i = 1 n δ X i , {\displaystyle \mathbb {P} _{n}=n^{-1}\sum _{i=1}^{n}\delta _{X_{i}},} where δ here stands for the Dirac measure. The empirical measure induces a map F → R {\displaystyle {\mathcal {F}}\to \mathbf {R} } given by: f ↦ P n f = 1 n ( f ( X 1 ) + . . . + f ( X n ) ) {\displaystyle f\mapsto \mathbb {P} _{n}f={\frac {1}{n}}(f(X_{1})+...+f(X_{n}))} Now suppose P is the underlying true distribution of the data, which is unknown. Empirical Processes theory aims at identifying classes F {\displaystyle {\mathcal {F}}} for which statements such as the following hold: uniform law of large numbers: ‖ P n − P ‖ F → n 0 , {\displaystyle \|\mathbb {P} _{n}-P\|_{\mathcal {F}}{\underset {n}{\to }}0,} That is, as n → ∞ {\displaystyle n\to \infty } , | 1 n ( f ( X 1 ) + . . . + f ( X n ) ) − ∫ f d P | → 0 {\displaystyle \left|{\frac {1}{n}}(f(X_{1})+...+f(X_{n}))-\int fdP\right|\to 0} uniformly for all f ∈ F {\displaystyle f\in {\mathcal {F}}} . uniform central limit theorem: G n = n ( P n − P ) ⇝ G , in ℓ ∞ ( F ) {\displaystyle \mathbb {G} _{n}={\sqrt {n}}(\mathbb {P} _{n}-P)\rightsquigarrow \mathbb {G} ,\quad {\text{in }}\ell ^{\infty }({\mathcal {F}})} In the former case F {\displaystyle {\mathcal {F}}} is called Glivenko–Cantelli class, and in the latter case (under the assumption ∀ x , sup f ∈ F | f ( x ) − P f | < ∞ {\displaystyle \forall x,\sup \nolimits _{f\in {\mathcal {F}}}\vert f(x)-Pf\vert <\infty } ) the class F {\displaystyle {\mathcal {F}}} is called Donsker or P-Donsker. A Donsker class is Glivenko–Cantelli in probability by an application of Slutsky's theorem. These statements are true for a single f {\displaystyle f} , by standard LLN, CLT arguments under regularity conditions, and the difficulty in the Empirical Processes comes in because joint statements are being made for all f ∈ F {\displaystyle f\in {\mathcal {F}}} . Intuitively then, the set F {\displaystyle {\mathcal {F}}} cannot be too large, and as it turns out that the geometry of F {\displaystyle {\mathcal {F}}} plays a very important role. One way of measuring how big the function set F {\displaystyle {\mathcal {F}}} is to use the so-called covering numbers. The covering number N ( ε , F , ‖ ⋅ ‖ ) {\displaystyle N(\varepsilon ,{\mathcal {F}},\|\cdot \|)} is the minimal number of balls { g : ‖ g − f ‖ < ε } {\displaystyle \{g:\|g-f\|<\varepsilon \}} needed to cover the set F {\displaystyle {\mathcal {F}}} (here it is obviously assumed that there is an underlying norm on F {\displaystyle {\mathcal {F}}} ). The entropy is the logarithm of the covering number. Two sufficient conditions are provided below, under which it can be proved that the set F {\displaystyle {\mathcal {F}}} is Glivenko–Cantelli or Donsker. A class F {\displaystyle {\mathcal {F}}} is P-Glivenko–Cantelli if it is P-measurable with envelope F such that P ∗ F < ∞ {\displaystyle P^{\ast }F<\infty } and satisfies: ∀ ε > 0 sup Q N ( ε ‖ F ‖ Q , F , L 1 ( Q ) ) < ∞ . {\displaystyle \forall \varepsilon >0\quad \sup \nolimits _{Q}N(\varepsilon \|F\|_{Q},{\mathcal {F}},L_{1}(Q))<\infty .} The next condition is a version of Dudley's theorem. If F {\displaystyle {\mathcal {F}}} is a class of functions such that ∫ 0 ∞ sup Q log ⁡ N ( ε ‖ F ‖ Q , 2 , F , L 2 ( Q ) ) d ε < ∞ {\displaystyle \int _{0}^{\infty }\sup \nolimits _{Q}{\sqrt {\log N\left(\varepsilon \|F\|_{Q,2},{\mathcal {F}},L_{2}(Q)\right)}}d\varepsilon <\infty } then F {\displaystyle {\mathcal {F}}} is P-Donsker for every probability measure P such that P ∗ F 2 < ∞ {\displaystyle P^{\ast }F^{2}<\infty } . In the last integral, the notation means ‖ f ‖ Q , 2 = ( ∫ | f | 2 d Q ) 1 2 {\displaystyle \|f\|_{Q,2}=\left(\int |f|^{2}dQ\right)^{\frac {1}{2}}} . === Symmetrization === The majority of the arguments about how to bound the empirical process rely on symmetrization, maximal and concentration inequalities, and chaining. Symmetrization is usually the first step of the proofs, and since it is used in many machine learning proofs on bounding empirical loss functions (including the proof of the VC inequality which is discussed in the next section). It is presented here: Consider the empirical process: f ↦ ( P n − P ) f = 1 n ∑ i = 1 n ( f ( X i ) − P f ) {\displaystyle f\mapsto (\mathbb {P} _{n}-P)f={\dfrac {1}{n}}\sum _{i=1}^{n}(f(X_{i})-Pf)} Turns out that there is a connection between the empirical and the following symmetrized process: f ↦ P n 0 f = 1 n ∑ i = 1 n ε i f ( X i ) {\displaystyle f\mapsto \mathbb {P} _{n}^{0}f={\dfrac {1}{n}}\sum _{i=1}^{n}\varepsilon _{i}f(X_{i})} The symmetrized process is a Rademacher process, conditionally on the data X i {\displaystyle X_{i}} . Therefore, it is a sub-Gaussian process by Hoeffding's inequality. Lemma (Symmetrization). For every nondecreasing, convex Φ: R → R and class of measurable functions F {\displaystyle {\mathcal {F}}} , E Φ ( ‖ P n − P ‖ F ) ≤ E Φ ( 2 ‖ P n 0 ‖ F ) {\displaystyle \mathbb {E} \Phi (\|\mathbb {P} _{n}-P\|_{\mathcal {F}})\leq \mathbb {E} \Phi \left(2\left\|\mathbb {P} _{n}^{0}\right\|_{\mathcal {F}}\right)} The proof of the Symmetrization lemma relies on introducing independent copies of the original variables X i {\displaystyle X_{i}} (sometimes referred to as a ghost sample) and replacing the inner expectation of the LHS by these copies. After an application of Jensen's inequality different signs could be introduced (hence the name symmetrization) without changing the expectation. The proof can be found below because of its instructive nature. The same proof method can be used to prove the Glivenko–Cantelli theorem. A typical way of proving empirical CLTs, first uses symmetrization to pass the empirical process to P n 0 {\displaystyle \mathbb {P} _{n}^{0}} and then argue conditionally on the data, using the fact that Rademacher processes are simple processes with nice properties. === VC Connection === It turns out that there is a fascinating connection between certain combinatorial properties of the set F {\displaystyle {\mathcal {F}}} and the entropy numbers. Uniform covering numbers can be controlled by the notion of Vapnik–Chervonenkis classes of sets – or shortly VC sets. Consider a collection C {\displaystyle {\mathcal {C}}} of subsets of the sample space X {\displaystyle

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