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Morphobank

MorphoBank is a web application for collaborative evolutionary research, specifically phylogenetic systematics or cladistics, on the phenotype. Historically, scientists conducting research on phylogenetic systematics have worked individually or in small groups employing traditional single-user software applications such as MacClade, Mesquite and Nexus Data Editor. As the hypotheses under study have grown more complex, large research teams have assembled to tackle the problem of discovering the Tree of Life for the estimated 4-100 million living species(Wilson 2003, pp. 77–80) and the many thousands more extinct species known from fossils. Because the phenotype is fundamentally visual, and as phenotype-based phylogenetic studies have continued to increase in size, it becomes important that observations be backed up by labeled images. Traditional desktop software applications currently in wide use do not provide robust support for team-based research or for image manipulation and storage. MorphoBank is a particularly important tool for the growing scientific field of phenomics. The development of MorphoBank, which began in 2001, has been funded by the National Science Foundation's Directorates for Geosciences, Biological Sciences and Computer and Information Science and Engineering. The significance of the scientific work on MorphoBank has been featured in the New York Times(here and here), among other publications. == Advantages == Teams of scientists studying phylogenetics to build the Tree of Life assemble large spreadsheets of observations about species (referred to as "matrices"). These teams require simultaneous access by each team member to a single and secure copy of the team's data during a scientific research project. This single copy of the data also changes with great frequency during the data collection phase. Images that can be very helpful for documenting homology statements must be displayed, labeled and shared as homology statements develop. This cannot be accomplished elegantly with a desktop software package alone because in a desktop environment each collaborator is working on his own private copy of project data. Changes made by one participant cannot automatically propagate to others, preventing collaborators from seeing each other's data edits until they are manually (and due to the effort involved, often only periodically) merged into a single "true" dataset. In all but the smallest and most disciplined of teams, file version control and the reconciliation of changes made on multiple copies of the data emerge quickly as significant drags on productivity. MorphoBank is an attempt to address these issues by leveraging the ubiquity of the web and modern web-based application techniques, including Ajax, web service layers, and rich web applications to provide a full-featured, net-accessible collaborative workspace for phylogenetic research. In particular, MorphoBank makes it easy to: Share all kinds of data with geographically separated team members, including taxonomy, character and specimen data, media (including images, video and audio), phylogenetic matrices (including data in the widely used NEXUS and TNT format) and other data such as documents and genetic sequences. Label high-resolution images using a web-based image annotation application. Collaboratively edit project data such as phylogenetic matrices using a built-in web-based matrix editor. The editor allows the linking of labeled images to individual cells of a matrix. Manage access to project data. Access ranges from full-access for team members to anonymous read-only access for potential reviewers. Publish completed project data on the web in support of a published paper with a persistent URL. Search The Encyclopedia of Life for taxon exemplar images. Store high resolution CT data Create ontologies for updating and populating matrix cells. These tasks are difficult or impossible in most existing software applications. == History == In 2001 the National Science Foundation (NSF) sponsored a workshop, at the American Museum of Natural History in New York to develop the outlines of a web-based system for a collaborative, media-rich research tool for morphological phylogenetics. An application prototype presented at the workshop was later refined with feedback from the workshop and became MorphoBank version 1.0. A grant from the US National Oceanic and Atmospheric Administration funded further revisions resulting in version 2.0, released in 2005. Current support from the NSF is funding current feature enhancements to MorphoBank. MorphoBank was hosted by Stony Brook University until late October 2021 and received back up support from the American Museum of Natural History. The current version is 3.0. Rationale for the software was described in the journal Cladistics. MorphoBank has also received support from NESCENT and the San Diego Supercomputer Center. Since 2018, MorphoBank has been supported in part by Phoenix Bioinformatics, a non-profit company founded to sustain databases for the basic sciences. A permanent move of MorphoBank from Stony Brook University to Phoenix Bioinformatics was complete in late October 2021. The San Diego Supercomputer Center has previously provided technical and hosting resources to the MorphoBank project. == Usage == MorphoBank hosts the products of peer-reviewed scientific research on phenotypes. An increasing volume of systematics data is "born digital" and MorphoBank is well suited to handle this type of material. On August 24, 2007, 62 active research projects were hosted by MorphoBank, as well as 6 completed (and published) projects. By 2017 over 2000 scientists and their students were registered content builders (users are not required to register and are even more numerous) and has more than 500 publicly available projects with approximately 80,000 images that are the products of scientific research. Over 1,500 active research projects are hosted by MorphoBank. The software has been used to assemble phylogenetic research on such groups as mammals, from bats to whales, bivalve molluscs, arachnids, fossil plants and living and extinct amniotes. It has also been used more broadly in evolutionary and paleontological research to host curated images associated with published research on lacewing insects geckos, raptor birds, dinosaurs, frogs and nematodes. MorphoBank is increasingly used in conjunction with the Paleobiology Database. Example published projects: Project 1097: Blank CE, 2013 Origin and early evolution of photosynthetic eukaryotes in freshwater environments – reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution Project 2520: Carvalho, T. P., R. E. Reis, and J. P. Friel, 2017 A new species of Hoplomyzon (Siluriformes: Aspredinidae) from Maracaibo Basin, Venezuela: osteological description using high-resolution Project 2651: Baron, M. G., Norman, D. B., Barrett, P. M., 2017 A new hypothesis of dinosaur relationships and early dinosaur evolution MorphoBank has been particularly important to the Assembling the Tree of Life initiative sponsored by the National Science Foundation. MorphoBank is well-suited to such projects because of its tools for merging taxonomic, character and matrix-based data, as well as its collaborative features. Highlights of this research include a collaborative matrix on mammal evolution published in Science that included over 4,000 phenomic characters scored for over 80 species, a matrix on extant baleen whales featuring nearly 600 images, and more.
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SIGMOD Edgar F. Codd Innovations Award

The ACM SIGMOD Edgar F. Codd Innovations Award is a lifetime research achievement award given by the ACM Special Interest Group on Management of Data, at its yearly flagship conference (also called SIGMOD). According to its homepage, it is given "for innovative and highly significant contributions of enduring value to the development, understanding, or use of database systems and databases". The award has been given since 1992. Until 2003, this award was known as the “SIGMOD Innovations Award.” In 2004, SIGMOD, with the unanimous approval of ACM Council, decided to rename the award to honor Dr. E.F. (Ted) Codd (1923 – 2003) who invented the relational data model and was responsible for the significant development of the database field as a scientific discipline. == Recipients ==
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Explore-then-commit algorithm

Explore Then Commit (ETC) is an algorithm for the multi-armed bandit problem foc,used on finding the best trade-off between exploration and exploitation. == Multi-armed bandit problem == The multi-armed bandit problem is a sequential game where one player has to choose at each turn between K {\displaystyle K} actions (arms). Behind every arm a {\displaystyle a} is an unknown distribution ν a {\displaystyle \nu _{a}} that lies in a set D {\displaystyle {\mathcal {D}}} known by the player (for example, D {\displaystyle {\mathcal {D}}} can be the set of Gaussian distributions or Bernoulli distributions). At each turn t {\displaystyle t} the player chooses (pulls) an arm a t {\displaystyle a_{t}} , they then get an observation X t {\displaystyle X_{t}} of the distribution ν a t {\displaystyle \nu _{a_{t}}} . === Regret minimization === The goal is to minimize the regret at time T {\displaystyle T} that is defined as R T := ∑ a = 1 K Δ a E [ N a ( T ) ] {\displaystyle R_{T}:=\sum _{a=1}^{K}\Delta _{a}\mathbb {E} [N_{a}(T)]} where μ a := E [ ν a ] {\displaystyle \mu _{a}:=\mathbb {E} [\nu _{a}]} is the mean of arm a {\displaystyle a} μ ∗ := max a μ a {\displaystyle \mu ^{}:=\max _{a}\mu _{a}} is the highest mean Δ a := μ ∗ − μ a {\displaystyle \Delta _{a}:=\mu ^{}-\mu _{a}} N a ( t ) {\displaystyle N_{a}(t)} is the number of pulls of arm a {\displaystyle a} up to turn t {\displaystyle t} The player has to find an algorithm that chooses at each turn t {\displaystyle t} which arm to pull based on the previous actions and observations ( a s , X s ) s < t {\displaystyle (a_{s},X_{s})_{s Read more →
Very large database

A very large database, (originally written very large data base) or VLDB, is a database that contains a very large amount of data, so much that it can require specialized architectural, management, processing and maintenance methodologies. == Definition == The vague adjectives of very and large allow for a broad and subjective interpretation, but attempts at defining a metric and threshold have been made. Early metrics were the size of the database in a canonical form via database normalization or the time for a full database operation like a backup. Technology improvements have continually changed what is considered very large. One definition has suggested that a database has become a VLDB when it is "too large to be maintained within the window of opportunity… the time when the database is quiet". == Sizes of a VLDB database == There is no absolute amount of data that can be cited. For example, one cannot say that any database with more than 1 TB of data is considered a VLDB. This absolute amount of data has varied over time as computer processing, storage and backup methods have become better able to handle larger amounts of data. That said, VLDB issues may start to appear when 1 TB is approached, and are more than likely to have appeared as 30 TB or so is exceeded. == VLDB challenges == Key areas where a VLDB may present challenges include configuration, storage, performance, maintenance, administration, availability and server resources. === Configuration === Careful configuration of databases that lie in the VLDB realm is necessary to alleviate or reduce issues raised by VLDB databases. === Administration === The complexities of managing a VLDB can increase exponentially for the database administrator as database size increases. === Availability and maintenance === When dealing with VLDB operations relating to maintenance and recovery such as database reorganizations and file copies which were quite practical on a non-VLDB take very significant amounts of time and resources for a VLDB database. In particular it typically infeasible to meet a typical recovery time objective (RTO), the maximum expected time a database is expected to be unavailable due to interruption, by methods which involve copying files from disk or other storage archives. To overcome these issues techniques such as clustering, cloned/replicated/standby databases, file-snapshots, storage snapshots or a backup manager may help achieve the RTO and availability, although individual methods may have limitations, caveats, license, and infrastructure requirements while some may risk data loss and not meet the recovery point objective (RPO). For many systems only geographically remote solutions may be acceptable. ==== Backup and recovery ==== Best practice is for backup and recovery to be architectured in terms of the overall availability and business continuity solution. === Performance === Given the same infrastructure there may typically be a decrease in performance, that is increase in response time as database size increases. Some accesses will simply have more data to process (scan) which will take proportionally longer (linear time); while the indexes used to access data may grow slightly in height requiring perhaps an extra storage access to reach the data (sub-linear time). Other effects can be caching becoming less efficient because proportionally less data can be cached and while some indexes such as the B+ automatically sustain well with growth others such as a hash table may need to be rebuilt. Should an increase in database size cause the number of accessors of the database to increase then more server and network resources may be consumed, and the risk of contention will increase. Some solutions to regaining performance include partitioning, clustering, possibly with sharding, or use of a database machine. ==== Partitioning ==== Partitioning may be able assist the performance of bulk operations on a VLDB including backup and recovery., bulk movements due to information lifecycle management (ILM), reducing contention as well as allowing optimization of some query processing. === Storage === In order to satisfy needs of a VLDB the database storage needs to have low access latency and contention, high throughput, and high availability. === Server resources === The increasing size of a VLDB may put pressure on server and network resources and a bottleneck may appear that may require infrastructure investment to resolve. == Relationship to big data == VLDB is not the same as big data, but the storage aspect of big data may involve a VLDB database. That said some of the storage solutions supporting big data were designed from the start to support large volumes of data, so database administrators may not encounter VLDB issues that older versions of traditional RDBMS's might encounter.
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Integrated writing environment

An integrated writing environment (IWE) is software that provides comprehensive writing and knowledge management functionality for writers and information workers. IWEs enable writers and information workers to perform a variety of tasks related to the document in the IWE in a single environment. This provides a distraction-free workspace and streamlined writing experience. IWEs provide similar efficiency and functionality benefits to writers and information professionals that integrated development environments (IDEs) provide to software developers. == Overview == IWEs are designed to maximize productivity and help improve the quality of written work by integrating together tools that allow users to work effectively in a single application. The IWE features may include integrated content search, reversion management, outlining, note management, and reference management, as may be suitable for the target field of use. == List of IWEs == Celtx This IWE is intended for screenplay writers and has screenplay writing and management tools. Celtex provides tools for the pre-production work phase, story development, storyboarding, script breakdowns, production scheduling, and reports. Scrivener This IWE targets novel, research paper, and script writing. Scrivener provides tools to organize notes and research documents for easy access and referencing. After completing the writing, Scrivener allows the user to export the document to formats supported by common word processors, such as Microsoft Word. TeXstudio This IWE targets LaTeX documents and provides interactive spelling checker, code folding, and syntax highlighting.
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BuildingSMART Data Dictionary

buildingSMART Data Dictionary (bSDD) is a service provided by buildingSMART which offers free data dictionaries for the international standardization of construction planning. The structure of bSDD was defined by the Nonprofit organization Buildingsmart and is used to describe objects and their attributes in a BIM process. == Aim == The aim of bSDD is to enable architects and planners to exchange and share building data across different specialists and language boundaries and thus avoid misunderstandings caused by different interpretations of terms. The bSDD standard extends the more general IFC. Software developers can access and use the dictionaries. In May 2025 over 300 dictionaries are available, including IFC, extensions to it such as Airport Domain IFC extension module or classification systems like Uniclass. == Structure == The main structural parts of bSDD are: Dictionary: A dictionary is a collection of classes: Class: A class describes the various object types, such as Bag drop or Baggage conveyor in airport planning. A class contains properties: Property: A property describes a part of a class, e.g. color or weight. Related properties are organized in a group: GroupOfProperties: A group organizes related properties, e.g. environmental properties or electrical properties. == Creating and managing a directory == Every dictionary in bSDD must be published in the name of a registered organization. As soon as the content is activated, it receives an unchangeable URI. This means that the content remains permanently in bSDD and cannot be deleted - this ensures stable use of the dictionary. It is only possible to change the status to inactive if it is no longer to be used - however, the dictionary remains permanently.
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Media aggregation platform

A Media Aggregation Platform or Media Aggregation Portal (MAP) is an over the top service for distributing web-based streaming media content from multiple sources to a large audience. MAPs consist of networks of sources who host their own content which viewers can choose and access directly from a larger variety of content to choose from than a single source can offer. The service is used by content providers, looking to extend the reach of their content. Unlike multichannel video programming distributor (MVPD) or multiple-system operators (MSO), MAPs rely on the Internet rather than cables or satellite. As more network television channels have moved online in the early 21st century, joining web-native channels like Netflix, MAPs aggregate content the way that MSOs and MVPDs have used cable, and to a lesser extent satellite and IPTV infrastructure. There are companies that offer a similar service for free, including Yidio and StreamingMoviesRight, while others charge a subscription fee like as FreeCast Inc's Rabbit TV Plus. When compared with MSOs and MVPDs, MAP networks have much lower costs due to lack of physical infrastructure. The majority of revenue from MAP services are retained by the content creators, and revenue is instead collected from advertisements, pay-per-view, and subscription-based content offerings instead of licensing and reselling content. MAP service consumers interact and purchase content directly from its source, without the markup added by a middleman.
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Rendezvous hashing

Rendezvous or highest random weight (HRW) hashing is an algorithm that allows clients to achieve distributed agreement on a set of k {\displaystyle k} options out of a possible set of n {\displaystyle n} options. A typical application is when clients need to agree on which sites (or proxies) objects are assigned to. Consistent hashing addresses the special case k = 1 {\displaystyle k=1} using a different method. Rendezvous hashing is both much simpler and more general than consistent hashing (see below). == History == Rendezvous hashing was invented by David Thaler and Chinya Ravishankar at the University of Michigan in 1996. Consistent hashing appeared a year later in the literature. Given its simplicity and generality, rendezvous hashing is now being preferred to consistent hashing in real-world applications. Rendezvous hashing was used very early on in many applications including mobile caching, router design, secure key establishment, and sharding and distributed databases. Other examples of real-world systems that use Rendezvous Hashing include the GitHub load balancer, the Apache Ignite distributed database, the Tahoe-LAFS file store, the CoBlitz large-file distribution service, Apache Druid, IBM's Cloud Object Store, the Arvados Data Management System, Apache Kafka, and the Twitter EventBus pub/sub platform. One of the first applications of rendezvous hashing was to enable multicast clients on the Internet (in contexts such as the MBONE) to identify multicast rendezvous points in a distributed fashion. It was used in 1998 by Microsoft's Cache Array Routing Protocol (CARP) for distributed cache coordination and routing. Some Protocol Independent Multicast routing protocols use rendezvous hashing to pick a rendezvous point. == Problem definition and approach == === Algorithm === Rendezvous hashing solves a general version of the distributed hash table problem: We are given a set of n {\displaystyle n} sites (servers or proxies, say). How can any set of clients, given an object O {\displaystyle O} , agree on a k-subset of sites to assign to O {\displaystyle O} ? The standard version of the problem uses k = 1. Each client is to make its selection independently, but all clients must end up picking the same subset of sites. This is non-trivial if we add a minimal disruption constraint, and require that when a site fails or is removed, only objects mapping to that site need be reassigned to other sites. The basic idea is to give each site S j {\displaystyle S_{j}} a score (a weight) for each object O i {\displaystyle O_{i}} , and assign the object to the highest scoring site. All clients first agree on a hash function h ( ⋅ ) {\displaystyle h(\cdot )} . For object O i {\displaystyle O_{i}} , the site S j {\displaystyle S_{j}} is defined to have weight w i , j = h ( O i , S j ) {\displaystyle w_{i,j}=h(O_{i},S_{j})} . Each client independently computes these weights w i , 1 , w i , 2 … w i , n {\displaystyle w_{i,1},w_{i,2}\dots w_{i,n}} and picks the k sites that yield the k largest hash values. The clients have thereby achieved distributed k {\displaystyle k} -agreement. If a site S {\displaystyle S} is added or removed, only the objects mapping to S {\displaystyle S} are remapped to different sites, satisfying the minimal disruption constraint above. The HRW assignment can be computed independently by any client, since it depends only on the identifiers for the set of sites S 1 , S 2 … S n {\displaystyle S_{1},S_{2}\dots S_{n}} and the object being assigned. HRW easily accommodates different capacities among sites. If site S k {\displaystyle S_{k}} has twice the capacity of the other sites, we simply represent S k {\displaystyle S_{k}} twice in the list, say, as S k , 1 , S k , 2 {\displaystyle S_{k,1},S_{k,2}} . Clearly, twice as many objects will now map to S k {\displaystyle S_{k}} as to the other sites. === Properties === Consider the simple version of the problem, with k = 1, where all clients are to agree on a single site for an object O. Approaching the problem naively, it might appear sufficient to treat the n sites as buckets in a hash table and hash the object name O into this table. Unfortunately, if any of the sites fails or is unreachable, the hash table size changes, forcing all objects to be remapped. This massive disruption makes such direct hashing unworkable. Under rendezvous hashing, however, clients handle site failures by picking the site that yields the next largest weight. Remapping is required only for objects currently mapped to the failed site, and disruption is minimal. Rendezvous hashing has the following properties: Low overhead: The hash function used is efficient, so overhead at the clients is very low. Load balancing: Since the hash function is randomizing, each of the n sites is equally likely to receive the object O. Loads are uniform across the sites. Site capacity: Sites with different capacities can be represented in the site list with multiplicity in proportion to capacity. A site with twice the capacity of the other sites will be represented twice in the list, while every other site is represented once. High hit rate: Since all clients agree on placing an object O into the same site SO, each fetch or placement of O into SO yields the maximum utility in terms of hit rate. The object O will always be found unless it is evicted by some replacement algorithm at SO. Minimal disruption: When a site fails, only the objects mapped to that site need to be remapped. Disruption is at the minimal possible level. Distributed k-agreement: Clients can reach distributed agreement on k sites simply by selecting the top k sites in the ordering. == O(log n) running time via skeleton-based hierarchical rendezvous hashing == The standard version of Rendezvous Hashing described above works quite well for moderate n, but when n {\displaystyle n} is extremely large, the hierarchical use of Rendezvous Hashing achieves O ( log ⁡ n ) {\displaystyle O(\log n)} running time. This approach creates a virtual hierarchical structure (called a "skeleton"), and achieves O ( log ⁡ n ) {\displaystyle O(\log n)} running time by applying HRW at each level while descending the hierarchy. The idea is to first choose some constant m {\displaystyle m} and organize the n {\displaystyle n} sites into c = ⌈ n / m ⌉ {\displaystyle c=\lceil n/m\rceil } clusters C 1 = { S 1 , S 2 … S m } , C 2 = { S m + 1 , S m + 2 … S 2 m } … {\displaystyle C_{1}=\left\{S_{1},S_{2}\dots S_{m}\right\},C_{2}=\left\{S_{m+1},S_{m+2}\dots S_{2m}\right\}\dots } Next, build a virtual hierarchy by choosing a constant f {\displaystyle f} and imagining these c {\displaystyle c} clusters placed at the leaves of a tree T {\displaystyle T} of virtual nodes, each with fanout f {\displaystyle f} . In the accompanying diagram, the cluster size is m = 4 {\displaystyle m=4} , and the skeleton fanout is f = 3 {\displaystyle f=3} . Assuming 108 sites (real nodes) for convenience, we get a three-tier virtual hierarchy. Since f = 3 {\displaystyle f=3} , each virtual node has a natural numbering in octal. Thus, the 27 virtual nodes at the lowest tier would be numbered 000 , 001 , 002 , . . . , 221 , 222 {\displaystyle 000,001,002,...,221,222} in octal (we can, of course, vary the fanout at each level - in that case, each node will be identified with the corresponding mixed-radix number). The easiest way to understand the virtual hierarchy is by starting at the top, and descending the virtual hierarchy. We successively apply Rendezvous Hashing to the set of virtual nodes at each level of the hierarchy, and descend the branch defined by the winning virtual node. We can in fact start at any level in the virtual hierarchy. Starting lower in the hierarchy requires more hashes, but may improve load distribution in the case of failures. For example, instead of applying HRW to all 108 real nodes in the diagram, we can first apply HRW to the 27 lowest-tier virtual nodes, selecting one. We then apply HRW to the four real nodes in its cluster, and choose the winning site. We only need 27 + 4 = 31 {\displaystyle 27+4=31} hashes, rather than 108. If we apply this method starting one level higher in the hierarchy, we would need 9 + 3 + 4 = 16 {\displaystyle 9+3+4=16} hashes to get to the winning site. The figure shows how, if we proceed starting from the root of the skeleton, we may successively choose the virtual nodes ( 2 ) 3 {\displaystyle (2)_{3}} , ( 20 ) 3 {\displaystyle (20)_{3}} , and ( 200 ) 3 {\displaystyle (200)_{3}} , and finally end up with site 74. The virtual hierarchy need not be stored, but can be created on demand, since the virtual nodes names are simply prefixes of base- f {\displaystyle f} (or mixed-radix) representations. We can easily create appropriately sorted strings from the digits, as required. In the example, we would be working with the strings 0 , 1 , 2 {\displaystyle 0,1,2} (at tier 1), 20 , 21 , 22 {\displaystyle 20,21,22} (at tier 2), and 200 , 201 , 202
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Data Science and Predictive Analytics

The first edition of the textbook Data Science and Predictive Analytics: Biomedical and Health Applications using R, authored by Ivo D. Dinov, was published in August 2018 by Springer. The second edition of the book was printed in 2023. This textbook covers some of the core mathematical foundations, computational techniques, and artificial intelligence approaches used in data science research and applications. By using the statistical computing platform R and a broad range of biomedical case-studies, the 23 chapters of the book first edition provide explicit examples of importing, exporting, processing, modeling, visualizing, and interpreting large, multivariate, incomplete, heterogeneous, longitudinal, and incomplete datasets (big data). == Structure == === First edition table of contents === The first edition of the Data Science and Predictive Analytics (DSPA) textbook is divided into the following 23 chapters, each progressively building on the previous content. === Second edition table of contents === The significantly reorganized revised edition of the book (2023) expands and modernizes the presented mathematical principles, computational methods, data science techniques, model-based machine learning and model-free artificial intelligence algorithms. The 14 chapters of the new edition start with an introduction and progressively build foundational skills to naturally reach biomedical applications of deep learning. Introduction Basic Visualization and Exploratory Data Analytics Linear Algebra, Matrix Computing, and Regression Modeling Linear and Nonlinear Dimensionality Reduction Supervised Classification Black Box Machine Learning Methods Qualitative Learning Methods—Text Mining, Natural Language Processing, and Apriori Association Rules Learning Unsupervised Clustering Model Performance Assessment, Validation, and Improvement Specialized Machine Learning Topics Variable Importance and Feature Selection Big Longitudinal Data Analysis Function Optimization Deep Learning, Neural Networks == Reception == The materials in the Data Science and Predictive Analytics (DSPA) textbook have been peer-reviewed in the Journal of the American Statistical Association, International Statistical Institute’s ISI Review Journal, and the Journal of the American Library Association. Many scholarly publications reference the DSPA textbook. As of January 17, 2021, the electronic version of the book first edition (ISBN 978-3-319-72347-1) is freely available on SpringerLink and has been downloaded over 6 million times. The textbook is globally available in print (hardcover and softcover) and electronic formats (PDF and EPub) in many college and university libraries and has been used for data science, computational statistics, and analytics classes at various institutions.
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Algorithm characterizations

Algorithm characterizations are attempts to formalize the word algorithm. Algorithm does not have a generally accepted formal definition. Researchers are actively working on this problem. This article will present some of the "characterizations" of the notion of "algorithm" in more detail. == The problem of definition == Over the last 200 years, the definition of the algorithm has become more complicated and detailed as researchers have tried to pin down the term. Indeed, there may be more than one type of "algorithm". But most agree that algorithm has something to do with defining generalized processes for the creation of "output" integers from other "input" integers – "input parameters" arbitrary and infinite in extent, or limited in extent but still variable—by the manipulation of distinguishable symbols (counting numbers) with finite collections of rules that a person can perform with paper and pencil. The most common number-manipulation schemes—both in formal mathematics and in routine life—are: (1) the recursive functions calculated by a person with paper and pencil, and (2) the Turing machine or its Turing equivalents—the primitive register-machine or "counter-machine" model, the random-access machine model (RAM), the random-access stored-program machine model (RASP) and its functional equivalent "the computer". When we are doing "arithmetic" we are really calculating by the use of "recursive functions" in the shorthand algorithms we learned in grade school, for example, adding and subtracting. The proofs that every "recursive function" we can calculate by hand we can compute by machine and vice versa—note the usage of the words calculate versus compute—is remarkable. But this equivalence together with the thesis (unproven assertion) that this includes every calculation/computation indicates why so much emphasis has been placed upon the use of Turing-equivalent machines in the definition of specific algorithms, and why the definition of "algorithm" itself often refers back to "the Turing machine". This is discussed in more detail under Stephen Kleene's characterization. The following are summaries of the more famous characterizations (Kleene, Markov, Knuth) together with those that introduce novel elements—elements that further expand the definition or contribute to a more precise definition. [ A mathematical problem and its result can be considered as two points in a space, and the solution consists of a sequence of steps or a path linking them. Quality of the solution is a function of the path. There might be more than one attribute defined for the path, e.g. length, complexity of shape, an ease of generalizing, difficulty, and so on. ] == Chomsky hierarchy == There is more consensus on the "characterization" of the notion of "simple algorithm". All algorithms need to be specified in a formal language, and the "simplicity notion" arises from the simplicity of the language. The Chomsky (1956) hierarchy is a containment hierarchy of classes of formal grammars that generate formal languages. It is used for classifying of programming languages and abstract machines. From the Chomsky hierarchy perspective, if the algorithm can be specified on a simpler language (than unrestricted), it can be characterized by this kind of language, else it is a typical "unrestricted algorithm". Examples: a "general purpose" macro language, like M4 is unrestricted (Turing complete), but the C preprocessor macro language is not, so any algorithm expressed in C preprocessor is a "simple algorithm". See also Relationships between complexity classes. == Features of a good algorithm == The following are desirable features of a well-defined algorithm, as discussed in Scheider and Gersting (1995): Unambiguous Operations: an algorithm must have specific, outlined steps. The steps should be exact enough to precisely specify what to do at each step. Well-Ordered: The exact order of operations performed in an algorithm should be concretely defined. Feasibility: All steps of an algorithm should be possible (also known as effectively computable). Input: an algorithm should be able to accept a well-defined set of inputs. Output: an algorithm should produce some result as an output, so that its correctness can be reasoned about. Finiteness: an algorithm should terminate after a finite number of instructions. Properties of specific algorithms that may be desirable include space and time efficiency, generality (i.e. being able to handle many inputs), or determinism. == 1881 John Venn's negative reaction to W. Stanley Jevons's Logical Machine of 1870 == In early 1870 W. Stanley Jevons presented a "Logical Machine" (Jevons 1880:200) for analyzing a syllogism or other logical form e.g. an argument reduced to a Boolean equation. By means of what Couturat (1914) called a "sort of logical piano [,] ... the equalities which represent the premises ... are "played" on a keyboard like that of a typewriter. ... When all the premises have been "played", the panel shows only those constituents whose sum is equal to 1, that is, ... its logical whole. This mechanical method has the advantage over VENN's geometrical method..." (Couturat 1914:75). For his part John Venn, a logician contemporary to Jevons, was less than thrilled, opining that "it does not seem to me that any contrivances at present known or likely to be discovered really deserve the name of logical machines" (italics added, Venn 1881:120). But of historical use to the developing notion of "algorithm" is his explanation for his negative reaction with respect to a machine that "may subserve a really valuable purpose by enabling us to avoid otherwise inevitable labor": (1) "There is, first, the statement of our data in accurate logical language", (2) "Then secondly, we have to throw these statements into a form fit for the engine to work with – in this case the reduction of each proposition to its elementary denials", (3) "Thirdly, there is the combination or further treatment of our premises after such reduction," (4) "Finally, the results have to be interpreted or read off. This last generally gives rise to much opening for skill and sagacity." He concludes that "I cannot see that any machine can hope to help us except in the third of these steps; so that it seems very doubtful whether any thing of this sort really deserves the name of a logical engine."(Venn 1881:119–121). == 1943, 1952 Stephen Kleene's characterization == This section is longer and more detailed than the others because of its importance to the topic: Kleene was the first to propose that all calculations/computations—of every sort, the totality of—can equivalently be (i) calculated by use of five "primitive recursive operators" plus one special operator called the mu-operator, or be (ii) computed by the actions of a Turing machine or an equivalent model. Furthermore, he opined that either of these would stand as a definition of algorithm. A reader first confronting the words that follow may well be confused, so a brief explanation is in order. Calculation means done by hand, computation means done by Turing machine (or equivalent). (Sometimes an author slips and interchanges the words). A "function" can be thought of as an "input-output box" into which a person puts natural numbers called "arguments" or "parameters" (but only the counting numbers including 0—the nonnegative integers) and gets out a single nonnegative integer (conventionally called "the answer"). Think of the "function-box" as a little man either calculating by hand using "general recursion" or computing by Turing machine (or an equivalent machine). "Effectively calculable/computable" is more generic and means "calculable/computable by some procedure, method, technique ... whatever...". "General recursive" was Kleene's way of writing what today is called just "recursion"; however, "primitive recursion"—calculation by use of the five recursive operators—is a lesser form of recursion that lacks access to the sixth, additional, mu-operator that is needed only in rare instances. Thus most of life goes on requiring only the "primitive recursive functions." === 1943 "Thesis I", 1952 "Church's Thesis" === In 1943 Kleene proposed what has come to be known as Church's thesis: "Thesis I. Every effectively calculable function (effectively decidable predicate) is general recursive" (First stated by Kleene in 1943 (reprinted page 274 in Davis, ed. The Undecidable; appears also verbatim in Kleene (1952) p.300) In a nutshell: to calculate any function the only operations a person needs (technically, formally) are the 6 primitive operators of "general" recursion (nowadays called the operators of the mu recursive functions). Kleene's first statement of this was under the section title "12. Algorithmic theories". He would later amplify it in his text (1952) as follows: "Thesis I and its converse provide the exact definition of the notion of a calculation (decision) procedure or algorithm, for the
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Information behavior

Information behavior is a field of information science research that seeks to understand the way people search for and use information in various contexts. It can include information seeking and information retrieval, but it also aims to understand why people seek information and how they use it. The term 'information behavior' was coined by Thomas D. Wilson in 1982 and sparked controversy upon its introduction. The term has now been adopted and Wilson's model of information behavior is widely cited in information behavior literature. In 2000, Wilson defined information behavior as "the totality of human behavior in relation to sources and channels of information". A variety of theories of information behavior seek to understand the processes that surround information seeking. An analysis of the most cited publications on information behavior during the early 21st century shows its theoretical nature. Information behavior research can employ various research methodologies grounded in broader research paradigms from psychology, sociology and education. In 2003, a framework for information-seeking studies was introduced that aims to guide the production of clear, structured descriptions of research objects and positions information-seeking as a concept within information behavior. == Concepts of information behavior == === Information need === Information need is a concept introduced by Wilson. Understanding the information need of an individual involved three elements: Why the individual decides to look for information, What purpose the information they find will serve, and How the information is used once it is retrieved === Information-seeking behavior === Information-seeking behavior is a more specific concept of information behavior. It specifically focuses on searching, finding, and retrieving information. Information-seeking behavior research can focus on improving information systems or, if it includes information need, can also focus on why the user behaves the way they do. A review study on information search behavior of users highlighted that behavioral factors, personal factors, product/service factors and situational factors affect information search behavior. Information-seeking behavior can be more or less explicit on the part of users: users might seek to solve some task or to establish some piece of knowledge which can be found in the data in question, or alternatively the search process itself is part of the objective of the user, in use cases for exploring visual content or for familiarising oneself with the content of an information service. In the general case, information-seeking needs to be understood and analysed as a session rather than as a one-off transaction with a search engine, and in a broader context which includes user high-level intentions in addition to the immediate information need. === Information use === An information need is the recognition that a gap exists in one’s knowledge, prompting a desire to seek information to fill that gap. It often arises when a person encounters a problem or question they cannot resolve with their current understanding. === Information poverty and barriers === Introduced by Elfreda Chatman in 1987, information poverty is informed by the understanding that information is not equally accessible to all people. Information poverty does not describe a lack of information, but rather a worldview in which one's own experiences inside their own small world may create a distrust in the information provided by those outside their own lived experiences. == Metatheories == In Library and Information Science (LIS), a metatheory is described "a set of assumptions that orient and direct theorizing about a given phenomenon". Library and information science researchers have adopted a number of different metatheories in their research. A common concern among LIS researchers, and a prominent discussion in the field, is the broad spectrum of theories that inform the study of information behavior, information users, or information use. This variation has been noted as a cause of concern because it makes individual studies difficult to compare or synthesize if they are not guided by the same theory. This sentiment has been expressed in studies of information behavior literature from the early 1980s and more recent literature reviews have declared it necessary to refine their reviews to specific contexts or situations due to the sheer breadth of information behavior research available. Below are descriptions of some, but not all, metatheories that have guided LIS research. === Cognitivist approach === A cognitive approach to understanding information behavior is grounded in psychology. It holds the assumption that a person's thinking influences how they seek, retrieve, and use information. Researchers that approach information behavior with the assumption that it is influenced by cognition, seek to understand what someone is thinking while they engage in information behavior and how those thoughts influence their behavior. Wilson's attempt to understand information-seeking behavior by defining information need includes a cognitive approach. Wilson theorizes that information behavior is influenced by the cognitive need of an individual. By understanding the cognitive information need of an individual, we may gain insight into their information behavior. Nigel Ford takes a cognitive approach to information-seeking, focusing on the intellectual processes of information-seeking. In 2004, Ford proposed an information-seeking model using a cognitive approach that focuses on how to improve information retrieval systems and serves to establish information-seeking and information behavior as concepts in and of themselves, rather than synonymous terms. === Constructionist approach === The constructionist approach to information behavior has roots in the humanities and social sciences. It relies on social constructionism, which assumes that a person's information behavior is influenced by their experiences in society. In order to understand information behavior, constructionist researchers must first understand the social discourse that surrounds the behavior. The most popular thinker referenced in constructionist information behavior research is Michel Foucault, who famously rejected the concept of a universal human nature. The constructionist approach to information behavior research creates space for contextualizing the behavior based on the social experiences of the individual. One study that approaches information behavior research through the social constructionist approach is a study of the information behavior of a public library knitting group. The authors use a collectivist theory to frame their research, which denies the universality of information behavior and focuses on "understanding the ways that discourse communities collectively construct information needs, seeking, sources, and uses". === Constructivist approach === The constructivist approach is born out of education and sociology in which, "individuals are seen as actively constructing an understanding of their worlds, heavily influenced by the social world(s) in which they are operating". Constructivist approaches to information behavior research generally treat the individual's reality as constructed within their own mind rather than built by the society in which they live. The constructivist metatheory makes space for the influence of society and culture with social constructivism, "which argues that, while the mind constructs reality in its relationship to the world, this mental process is significantly informed by influences received from societal conventions, history and interaction with significant others". == Theories == A common concern among LIS researchers, and a prominent discussion in the field, is the broad spectrum of theories that inform LIS research. This variation has been noted as a cause of concern because it makes individual studies difficult to compare if they are not guided by the same theory. Recent studies have shown that the impact of these theories and theoretical models is very limited. LIS researchers have applied concepts and theories from many disciplines, including sociology, psychology, communication, organizational behavior, and computer science. === Wilson's theory of information behavior (1981) === The term was coined by Thomas D. Wilson in his 1981 paper, on the grounds that the current term, 'information needs' was unhelpful since 'need' could not be directly observed, while how people behaved in seeking information could be observed and investigated. However, there is increasing work in the information-searching field that is relating behaviors to underlying needs. In 2000, Wilson described information behavior as the totality of human behavior in relation to sources and channels of information, including both active and passive information-seeking, and information use. He described info
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Algorithmic paradigm

An algorithmic paradigm or algorithm design paradigm is a generic model or framework which underlies the design of a class of algorithms. An algorithmic paradigm is an abstraction higher than the notion of an algorithm, just as an algorithm is an abstraction higher than a computer program. == List of well-known paradigms == === General === Backtracking Branch and bound Brute-force search Divide and conquer Dynamic programming Greedy algorithm Recursion Prune and search === Parameterized complexity === Kernelization Iterative compression === Computational geometry === Sweep line algorithms Rotating calipers Randomized incremental construction
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You.com

You.com is an artificial intelligence search startup that has pivoted away from consumer search engine operations toward business-focused AI tools and APIs. The company was founded in 2020 by Richard Socher, the former chief scientist at Salesforce, and Bryan McCann, a former NLP researcher at Salesforce. == History == Following its 2020 founding, You.com opened its public beta on November 9, 2021, and received $20 million in funding led by Salesforce founder and CEO Marc Benioff. Other investors include Breyer Capital, Sound Ventures, and Day One Ventures. The domain You.com was initially purchased in 1996 by Benioff. Benioff invested in You.com and transferred ownership of the You.com domain name to the company. In July 2022, You.com announced its $25 million Series A funding round led by Radical Ventures with participation from Time Ventures, Breyer Capital, Norwest Venture Partners and Day One Ventures. In September 2024, You.com raised $50 million in Series B funding led by Georgian. In September 2025, You.com raised $100 million in Series C funding led by Cox Enterprises at a $1.5 billion valuation, achieving unicorn status. == Business model == You.com generates revenue primarily through enterprise sales of search APIs and AI tools. The platform provides web search capabilities that can be integrated into enterprise applications and AI agents. == Features == On December 23, 2022, You.com was the first search engine to launch an LLM chatbot with live web results alongside its responses. Initially known as YouChat, the chatbot was primarily based on the GPT-3.5 large language model and could answer questions, suggest ideas, translate text, summarize articles, compose emails, and write code snippets, while staying up-to-date with current events and citing sources. Several further versions of YouChat were released. The second version, called YouChat 2.0, was released on February 7, 2023, incorporated improved conversational AI and community-built applications by blending a large language model named C-A-L (Chat, Apps, and Links). This update enabled YouChat to provide results in various formats, such as charts, photos, videos, tables, graphs, text or code, so users can find answers without leaving the search results page. YouChat 3.0, unveiled on May 4, 2023, combined chat functionality with results from Reddit, TikTok, Stack Overflow and Wikipedia. === YouPro === On June 21, 2023, You.com introduced YouPro, a paid subscription. Both free and paid versions provide access to large language models connected to the internet with citation capabilities. === ARI === In February 2025, You.com launched ARI (Advanced Research and Insights), a deep research agent that scans over 400 sources simultaneously to produce research reports with verified citations and interactive graphs, charts, and visualizations. The platform targets regulated industries where comprehensive source verification is critical, with customers including healthcare publishers and advisory firms. == Reception == You.com was named one of TIME's Best Inventions of 2022. You.com's ARI (Advanced Research & Insights) feature was named one of TIME's Best Inventions of 2025.
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Schema crosswalk

A schema crosswalk is a table that shows equivalent elements (or "fields") in more than one database schema. It maps the elements in one schema to the equivalent elements in another. Crosswalk tables are often employed within or in parallel to enterprise systems, especially when multiple systems are interfaced or when the system includes legacy system data. In the context of Interfaces, they function as an internal extract, transform, load (ETL) mechanism. For example, this is a metadata crosswalk from MARC standards to Dublin Core: Crosswalks show people where to put the data from one scheme into a different scheme. They are often used by libraries, archives, museums, and other cultural institutions to translate data to or from MARC standards, Dublin Core, Text Encoding Initiative (TEI), and other metadata schemes. For example, an archive has a MARC record in its catalog describing a manuscript. Suppose the archive makes a digital copy of that manuscript and wants to display it on the web along with the information from the catalog. In that case, it will have to translate the data from the MARC catalog record into a different format, such as Metadata Object Description Schema, that is viewable on a webpage. Because MARC has various fields than MODS, decisions must be made about where to put the data into MODS. This type of "translating" from one format to another is often called "metadata mapping" or "field mapping," and is related to "data mapping", and "semantic mapping". Crosswalks also have several technical capabilities. They help databases using different metadata schemes to share information. They help metadata harvesters create union catalogs. They enable search engines to search multiple databases simultaneously with a single query. == Challenges for crosswalks == One of the biggest challenges for crosswalks is that no two metadata schemes are 100% equivalent. One scheme may have a field that doesn't exist in another scheme or a field that is split into two different fields in another scheme; this is why data is often lost when mapping from a complex scheme to a simpler one. For example, when mapping from MARC to Simple Dublin Core, the distinction between types of titles is lost: Simple Dublin Core only has one "Title" element, so all of the different types of MARC titles get lumped together without further distinctions. A future attempt to convert the metadata back into MARC would enter the information in the basic MARC 245 Title Statement field, with none of the original distinctions. This is why crosswalks are said to be "lateral" (one-way) mappings from one scheme to another. Separate crosswalks would be required to map from scheme A to scheme B and from scheme B to scheme A. === Difficulties in mapping === Other mapping problems arise when: One scheme has one element that needs to be split up with different parts of it placed in multiple other elements in the second scheme ("one-to-many" mapping) One scheme allows an element to be repeated more than once while another only allows that element to appear once with multiple terms in it Schemes have different data formats (e.g. John Doe or Doe, John) An element in one scheme is indexed, but the equivalent element in the other scheme is not Schemes may use different controlled vocabularies Schemes change their standards over time Some of these problems are not fixable. As Karen Coyle says in "Crosswalking Citation Metadata: The University of California's Experience," "The more metadata experience we have, the more it becomes clear that metadata perfection is not attainable, and anyone who attempts it will be sorely disappointed. When metadata is crosswalked between two or more unrelated sources, there will be data elements that cannot be reconciled in an ideal manner. The key to a successful metadata crosswalk is intelligent flexibility. It is essential to focus on the important goals and be willing to compromise to reach a practical conclusion to projects."
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Collision problem

The r-to-1 collision problem is an important theoretical problem in complexity theory, quantum computing, and computational mathematics. The collision problem most often refers to the 2-to-1 version: given n {\displaystyle n} even and a function f : { 1 , … , n } → { 1 , … , n } {\displaystyle f:\,\{1,\ldots ,n\}\rightarrow \{1,\ldots ,n\}} , we are promised that f is either 1-to-1 or 2-to-1. We are only allowed to make queries about the value of f ( i ) {\displaystyle f(i)} for any i ∈ { 1 , … , n } {\displaystyle i\in \{1,\ldots ,n\}} . The problem then asks how many such queries we need to make to determine with certainty whether f is 1-to-1 or 2-to-1. == Classical solutions == === Deterministic === Solving the 2-to-1 version deterministically requires n 2 + 1 {\textstyle {\frac {n}{2}}+1} queries, and in general distinguishing r-to-1 functions from 1-to-1 functions requires n r + 1 {\textstyle {\frac {n}{r}}+1} queries. This is a straightforward application of the pigeonhole principle: if a function is r-to-1, then after n r + 1 {\textstyle {\frac {n}{r}}+1} queries we are guaranteed to have found a collision. If a function is 1-to-1, then no collision exists. Thus, n r + 1 {\textstyle {\frac {n}{r}}+1} queries suffice. If we are unlucky, then the first n / r {\displaystyle n/r} queries could return distinct answers, so n r + 1 {\textstyle {\frac {n}{r}}+1} queries is also necessary. === Randomized === If we allow randomness, the problem is easier. By the birthday paradox, if we choose (distinct) queries at random, then with high probability we find a collision in any fixed 2-to-1 function after Θ ( n ) {\displaystyle \Theta ({\sqrt {n}})} queries. == Quantum solution == The BHT algorithm, which uses Grover's algorithm, solves this problem optimally by only making O ( n 1 / 3 ) {\displaystyle O(n^{1/3})} queries to f. The matching lower bound of Ω ( n 1 / 3 ) {\displaystyle \Omega (n^{1/3})} was proved by Aaronson and Shi using the polynomial method.
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