Telenet was an American commercial packet-switched network which went into service in August 16, 1975. It was the first FCC-licensed public data network in the United States. Various commercial and government interests paid monthly fees for dedicated lines connecting their computers and local networks to this backbone network. Free public dialup access to Telenet, for those who wished to access these systems, was provided in hundreds of cities throughout the United States. == History == After establishing that commercial operation of "value added carriers" was legal in the U.S., Bolt Beranek and Newman (BBN), who were the private contractors for constructing packet switching nodes (Interface Message Processor) for the ARPANET, set out to create a private sector version. The original founding company, Telenet Inc., was established by BBN. In January 1975, Telenet Communications Corporation announced that they had acquired the necessary venture capital after a two-year quest. Initially, Bob Kahn was the first President of Telenet; he then moved to ARPA as Larry Roberts left to become President of the company. Barry Wessler also joined from ARPA. On August 16 of the same year they began operating the first public data network. The network offered an email service called Telemail. Telenet had its first offices in downtown Washington, D.C., then moved to McLean, Virginia. It was acquired by GTE in 1979, and then moved to offices in Reston, Virginia. It was later acquired by Sprint and called "Sprintnet". Sprint migrated customers from Telenet to the modern-day Sprintlink IP network, one of many networks composing today's Internet. == Coverage == Originally, the public network had switching nodes in seven US cities: Washington, D.C. (network operations center as well as switching) Boston, Massachusetts New York, New York Chicago, Illinois Dallas, Texas San Francisco, California Los Angeles, California The switching nodes were fed by Telenet Access Controller (TAC) terminal concentrators both colocated and remote from the switches. By 1980, there were over 1000 switches in the public network. At that time, the next largest network using Telenet switches was that of Southern Bell, which had approximately 250 switches. In 1977, Telenet added a London node and a Network Control Centre in a London building of Britain's Post Office Telecommunications. == Internal network technology == Telenet initially used a proprietary virtual connection host interface. The network used statically defined hop-by-hop routing, using Prime commercial minicomputers as switches, but then migrated to a purpose-built multiprocessing switch based on 6502 microprocessors. Among the innovations of this second-generation switch was a patented arbitrated bus interface that created a switched fabric among the microprocessors. By contrast, a typical microprocessor-based system of the time used a bus; switched fabrics did not become common until about twenty years later, with the advent of PCI Express and HyperTransport. Most interswitch lines ran at 56 kbit/s, with a few, such as New York-Washington, at T1 (i.e., 1.544 Mbit/s). Originally, the switching tables could not be altered separately from the main executable code, and topology updates had to be made by deliberately crashing the switch code and forcing a reboot from the network management center. Improvements in the software allowed new tables to be loaded, but the network never used dynamic routing protocols. Multiple static routes, on a switch-by-switch basis, could be defined for fault tolerance. Network management functions continued to run on Prime minicomputers. Roberts and Barry Wessler joined the international effort to standardize the a protocol for packet-switched data communication based on virtual circuits shortly before it was finalized. The CCITT proposal for X.25 was being prepared by Rémi Després and other international experts. A few minor changes, which complemented the proposed specification, were accommodated to enable Telenet to join the agreement. Telenet adopted X.25 shortly after the protocol was published in March 1976. Its X.25 host interface was the first in the industry. The main internal protocol was a proprietary variant on X.75; Telenet also ran standard X.75 gateways to other packet switching networks. == Accessing the network == === Basic asynchronous access === Users could use modems on the Public Switched Telephone Network to dial TAC ports, calling either from "dumb" terminals or from computers emulating such terminals. Organizations with a large number of local terminals could install a TAC on their own site, which used a dedicated line, at up to 56 kbit/s, to connect to a switch at the nearest Telenet location. Dialup modems supported had a maximum speed of 1200 bit/s, and later 4800 bit/s. For example, a customer in NYC could dial into the local number, then type in a command similar to: which would connect (that "c") them to a computer system designated as number "555" located in the same vicinity as the standard telephone "area code" 301. One significant customer was an early (what would now be called) internet service provider The Source which had their equipment in Mclean, Va. Telenet offered a much lower nighttime rate when there were few corporate customers, and this let The Source set up a modestly priced offering to tens of thousands of customers. Another prominent customer in the 1980s was Quantum Link (now AOL). === Other access protocols === Telenet supported remote concentrators for IBM 3270 family intelligent terminals, which communicated, via X.25 to Telenet-written software that ran in IBM 370x series front-end processors. Telenet also supported Block Mode Terminal Interfaces (BMTI) for IBM Remote Job Entry terminals supporting the 2780/3780 and HASP Bisync protocols. === PC Pursuit === In the late 1980s, Telenet offered a service called PC Pursuit. For a flat monthly fee, customers could dial into the Telenet network in one city, then dial out on the modems in another city to access bulletin board systems and other services. PC Pursuit was popular among computer hobbyists because it sidestepped long-distance charges. In this sense, PC Pursuit was similar to the Internet, allowing any user to call any system as if it were local. On connection to the network, the user entered a 5-letter code for the target city they wished to call. This consisted of a 2-letter state code and a 3-letter acronym for the city. For instance, to call a system in Cleveland, Ohio, the user would enter the code OHCLV, for "OHio", "CLeVeland". Once connected, the user could dial out to any local number, and the system simulated a direct connection between the two endpoints.
Focus recovery based on the linear canonical transform
For digital image processing, the Focus recovery from a defocused image is an ill-posed problem since it loses the component of high frequency. Most of the methods for focus recovery are based on depth estimation theory. The Linear canonical transform (LCT) gives a scalable kernel to fit many well-known optical effects. Using LCTs to approximate an optical system for imaging and inverting this system, theoretically permits recovery of a defocused image. == Depth of field and perceptual focus == In photography, depth of field (DOF) means an effective focal length. It is usually used for stressing an object and deemphasizing the background (and/or the foreground). The important measure related to DOF is the lens aperture. Decreasing the diameter of aperture increases focus and lowers resolution and vice versa. == The Huygens–Fresnel principle and DOF == The Huygens–Fresnel principle describes diffraction of wave propagation between two fields. It belongs to Fourier optics rather than geometric optics. The disturbance of diffraction depends on two circumstance parameters, the size of aperture and the interfiled distance. Consider a source field and a destination field, field 1 and field 0, respectively. P1(x1,y1) is the position in the source field, P0(x0,y0) is the position in the destination field. The Huygens–Fresnel principle gives the diffraction formula for two fields U(x0,y0), U(x1,y1) as following: U ( x 0 , y 0 ) = 1 j λ ∫ ∫ U ( x 1 , y 1 ) e j k r 01 r 01 cos θ d x 1 d y 1 {\displaystyle \mathbf {U} (x_{0},y_{0})={\frac {1}{j\lambda }}\int \!\int \mathbf {U} (x_{1},y_{1}){\frac {e^{jkr_{01}}}{r_{01}}}\cos \theta dx_{1}dy_{1}} where θ denotes the angle between r 01 {\displaystyle r_{01}} and z {\displaystyle z} . Replace cos θ by r 01 z {\displaystyle {\frac {r_{01}}{z}}} and r 01 {\displaystyle r_{01}} by [ ( x 0 − x 1 ) 2 + ( y 0 − y 1 ) 2 + z 2 ] 1 / 2 {\displaystyle [(x_{0}-x_{1})^{2}+(y_{0}-y_{1})^{2}+z^{2}]^{1/2}} we get U ( x 0 , y 0 ) = 1 j λ z ∫ ∫ U ( x 1 , y 1 ) exp ( j k z [ 1 + ( x 0 − x 1 z ) 2 + ( y 0 − y 1 z ) 2 ] 1 / 2 ) 1 + ( x 0 − x 1 z ) 2 + ( y 0 − y 1 z ) 2 d x 1 d y 1 {\displaystyle \mathbf {U} (x_{0},y_{0})={\frac {1}{j\lambda z}}\int \!\int \mathbf {U} (x_{1},y_{1}){\frac {\exp(jkz[1+({\frac {x_{0}-x_{1}}{z}})^{2}+({\frac {y_{0}-y_{1}}{z}})^{2}]^{1/2})}{1+({\frac {x_{0}-x_{1}}{z}})^{2}+({\frac {y_{0}-y_{1}}{z}})^{2}}}dx_{1}dy_{1}} The further distance z or the smaller aperture (x1,y1) causes a greater diffraction. A larger DOF can lead to a more effective focused wave distribution. This seems to be a conflict. Here are the notations: Diffraction In a real imaging environment, the depths of objects comparing to the aperture are usually not enough to lead to serious diffraction. However, a long enough depth of the object can truly blurs the image. Effective Focus Small aperture, small blurring radius, few wave information. Loses details in comparing to a large aperture. In conclusion, diffraction explains a micro behavior whereas DOF shows a macro behavior. Both of them are related to aperture size. == Linear canonical transform == As the meaning of "canonical", the linear canonical transform (LCT) is a scalable transform that connects to many important kernels such as the Fresnel transform, Fraunhofer transform and the fractional Fourier transform. It can be easily controlled by its four parameters, a, b, c, d (3 degrees of freedom). The definition: L M ( f ( u ) ) = ∫ L M ( u , u ′ ) f ( u ′ ) d u ′ {\displaystyle L_{M}(f(u))=\int L_{M}(u,u')f(u')du'} where L M ( u , u ′ ) = { 1 b e − j π / 4 e [ j π ( d b u 2 ) − 2 1 b u u ′ + a b u ′ 2 ] , if b ≠ 0 d e j 2 c d u 2 δ ( u ′ − d u ) , if b = 0 {\displaystyle L_{M}(u,u')={\begin{cases}{\sqrt {\frac {1}{b}}}e^{-j\pi /4}e^{[j\pi ({\frac {d}{b}}u^{2})-2{\frac {1}{b}}uu'+{\frac {a}{b}}u'^{2}]},&{\mbox{if }}b\neq 0\\{\sqrt {d}}e^{{\frac {j}{2}}cdu^{2}}\delta (u'-du),&{\mbox{if }}b=0\end{cases}}} Consider a general imaging system with object distance z0, focal length of the thin lens f and an imaging distance z1. The effect of the propagation in freespace acts as nearly a chirp convolution, that is, the formula of diffraction. Besides, the effect of the propagation in thin lens acts as a chirp multiplication. The parameters are all simplified as paraxial approximations while meeting the freespace propagation. It does not consider aperture size. From the properties of the LCT, it is possible to obtain those 4 parameters for this optical system as: [ 1 − z 1 f λ z 0 − λ z 0 z 1 f + λ z 1 − 1 λ f 1 − z 0 f ] {\displaystyle {\begin{bmatrix}1-{\frac {z_{1}}{f}}\quad &\lambda z_{0}-{\frac {\lambda z_{0}z_{1}}{f}}+\lambda z_{1}\\-{\frac {1}{\lambda f}}\quad &1-{\frac {z_{0}}{f}}\end{bmatrix}}} Once the values of z1, z0 and f are known, the LCT can simulate any optical system.
EfficientNet
EfficientNet is a family of convolutional neural networks (CNNs) for computer vision published by researchers at Google AI in 2019. Its key innovation is compound scaling, which uniformly scales all dimensions of depth, width, and resolution using a single parameter. EfficientNet models have been adopted in various computer vision tasks, including image classification, object detection, and segmentation. == Compound scaling == EfficientNet introduces compound scaling, which, instead of scaling one dimension of the network at a time, such as depth (number of layers), width (number of channels), or resolution (input image size), uses a compound coefficient ϕ {\displaystyle \phi } to scale all three dimensions simultaneously. Specifically, given a baseline network, the depth, width, and resolution are scaled according to the following equations: depth multiplier: d = α ϕ width multiplier: w = β ϕ resolution multiplier: r = γ ϕ {\displaystyle {\begin{aligned}{\text{depth multiplier: }}d&=\alpha ^{\phi }\\{\text{width multiplier: }}w&=\beta ^{\phi }\\{\text{resolution multiplier: }}r&=\gamma ^{\phi }\end{aligned}}} subject to α ⋅ β 2 ⋅ γ 2 ≈ 2 {\displaystyle \alpha \cdot \beta ^{2}\cdot \gamma ^{2}\approx 2} and α ≥ 1 , β ≥ 1 , γ ≥ 1 {\displaystyle \alpha \geq 1,\beta \geq 1,\gamma \geq 1} . The α ⋅ β 2 ⋅ γ 2 ≈ 2 {\displaystyle \alpha \cdot \beta ^{2}\cdot \gamma ^{2}\approx 2} condition is such that increasing ϕ {\displaystyle \phi } by a factor of ϕ 0 {\displaystyle \phi _{0}} would increase the total FLOPs of running the network on an image approximately 2 ϕ 0 {\displaystyle 2^{\phi _{0}}} times. The hyperparameters α {\displaystyle \alpha } , β {\displaystyle \beta } , and γ {\displaystyle \gamma } are determined by a small grid search. The original paper suggested 1.2, 1.1, and 1.15, respectively. Architecturally, they optimized the choice of modules by neural architecture search (NAS), and found that the inverted bottleneck convolution (which they called MBConv) used in MobileNet worked well. The EfficientNet family is a stack of MBConv layers, with shapes determined by the compound scaling. The original publication consisted of 8 models, from EfficientNet-B0 to EfficientNet-B7, with increasing model size and accuracy. EfficientNet-B0 is the baseline network, and subsequent models are obtained by scaling the baseline network by increasing ϕ {\displaystyle \phi } . == Variants == EfficientNet has been adapted for fast inference on edge TPUs and centralized TPU or GPU clusters by NAS. EfficientNet V2 was published in June 2021. The architecture was improved by further NAS search with more types of convolutional layers. It also introduced a training method, which progressively increases image size during training, and uses regularization techniques like dropout, RandAugment, and Mixup. The authors claim this approach mitigates accuracy drops often associated with progressive resizing.
Dynamic epistemic logic
Dynamic epistemic logic (DEL) is a logical framework dealing with knowledge and information change. Typically, DEL focuses on situations involving multiple agents and studies how their knowledge changes when events occur. These events can change factual properties of the actual world (they are called ontic events): for example a red card is painted in blue. They can also bring about changes of knowledge without changing factual properties of the world (they are called epistemic events): for example, a card is revealed publicly (or privately) to be red. Originally, DEL focused on epistemic events. Only some of the basic ideas are present in this entry of the original DEL framework; more details about DEL in general can be found in the references. Due to the nature of its object of study and its abstract approach, DEL is related and has applications to numerous research areas, such as computer science (artificial intelligence), philosophy (formal epistemology), economics (game theory) and cognitive science. In computer science, DEL is for example very much related to multi-agent systems, which are systems where multiple intelligent agents interact and exchange information. As a combination of dynamic logic and epistemic logic, dynamic epistemic logic is a young field of research. It really started in 1989 with Plaza's logic of public announcement. Independently, Gerbrandy and Groeneveld proposed a system dealing moreover with private announcement and that was inspired by the work of Veltman. Another system was proposed by van Ditmarsch whose main inspiration was the Cluedo game. But the most influential and original system was the system proposed by Baltag, Moss and Solecki. This system can deal with all the types of situations studied in the works above and its underlying methodology is conceptually grounded. This entry will present some of its basic ideas. Formally, DEL extends ordinary epistemic logic by the inclusion of event models to describe actions, and a product update operator that defines how epistemic models are updated as the consequence of executing actions described through event models. Epistemic logic will first be recalled. Then, actions and events will enter into the picture and we will introduce the DEL framework. == Epistemic logic == Epistemic logic is a modal logic dealing with the notions of knowledge and belief. As a logic, it is concerned with understanding the process of reasoning about knowledge and belief: which principles relating the notions of knowledge and belief are intuitively plausible? Like epistemology, it stems from the Greek word ϵ π ι σ τ η μ η {\displaystyle \epsilon \pi \iota \sigma \tau \eta \mu \eta } or ‘episteme’ meaning knowledge. Epistemology is nevertheless more concerned with analyzing the very nature and scope of knowledge, addressing questions such as “What is the definition of knowledge?” or “How is knowledge acquired?”. In fact, epistemic logic grew out of epistemology in the Middle Ages thanks to the efforts of Burley and Ockham. The formal work, based on modal logic, that inaugurated contemporary research into epistemic logic dates back only to 1962 and is due to Hintikka. It then sparked in the 1960s discussions about the principles of knowledge and belief and many axioms for these notions were proposed and discussed. For example, the interaction axioms K p → B p {\displaystyle Kp\rightarrow Bp} and B p → K B p {\displaystyle Bp\rightarrow KBp} are often considered to be intuitive principles: if an agent Knows p {\displaystyle p} then (s)he also Believes p {\displaystyle p} , or if an agent Believes p {\displaystyle p} , then (s)he Knows that (s)he Believes p {\displaystyle p} . More recently, these kinds of philosophical theories were taken up by researchers in economics, artificial intelligence and theoretical computer science where reasoning about knowledge is a central topic. Due to the new setting in which epistemic logic was used, new perspectives and new features such as computability issues were then added to the research agenda of epistemic logic. === Syntax === In the sequel, A G T S = { 1 , … , n } {\displaystyle AGTS=\{1,\ldots ,n\}} is a finite set whose elements are called agents and P R O P {\displaystyle PROP} is a set of propositional letters. The epistemic language is an extension of the basic multi-modal language of modal logic with a common knowledge operator C A {\displaystyle C_{A}} and a distributed knowledge operator D A {\displaystyle D_{A}} . Formally, the epistemic language L EL C {\displaystyle {\mathcal {L}}_{\textsf {EL}}^{C}} is defined inductively by the following grammar in BNF: L EL C : ϕ ::= p ∣ ¬ ϕ ∣ ( ϕ ∧ ϕ ) ∣ K j ϕ ∣ C A ϕ ∣ D A ϕ {\displaystyle {\mathcal {L}}_{\textsf {EL}}^{C}:\phi ~~::=~~p~\mid ~\neg \phi ~\mid ~(\phi \land \phi )~\mid ~K_{j}\phi ~\mid ~C_{A}\phi ~\mid ~D_{A}\phi } where p ∈ P R O P {\displaystyle p\in PROP} , j ∈ A G T S {\displaystyle j\in {AGTS}} and A ⊆ A G T S {\displaystyle A\subseteq {AGTS}} . The basic epistemic language L E L {\displaystyle {\mathcal {L}}_{EL}} is the language L E L C {\displaystyle {\mathcal {L}}_{EL}^{C}} without the common knowledge and distributed knowledge operators. The formula ⊥ {\displaystyle \bot } is an abbreviation for ¬ p ∧ p {\displaystyle \neg p\land p} (for a given p ∈ P R O P {\displaystyle p\in PROP} ), ⟨ K j ⟩ ϕ {\displaystyle \langle K_{j}\rangle \phi } is an abbreviation for ¬ K j ¬ ϕ {\displaystyle \neg K_{j}\neg \phi } , E A ϕ {\displaystyle E_{A}\phi } is an abbreviation for ⋀ j ∈ A K j ϕ {\displaystyle \bigwedge \limits _{j\in A}K_{j}\phi } and C ϕ {\displaystyle C\phi } an abbreviation for C A G T S ϕ {\displaystyle C_{AGTS}\phi } . Group notions: general, common and distributed knowledge. In a multi-agent setting there are three important epistemic concepts: general knowledge, distributed knowledge and common knowledge. The notion of common knowledge was first studied by Lewis in the context of conventions. It was then applied to distributed systems and to game theory, where it allows to express that the rationality of the players, the rules of the game and the set of players are commonly known. General knowledge. General knowledge of ϕ {\displaystyle \phi } means that everybody in the group of agents A G T S {\displaystyle {AGTS}} knows that ϕ {\displaystyle \phi } . Formally, this corresponds to the following formula: E ϕ := ⋀ j ∈ A G T S K j ϕ . {\displaystyle E\phi :={\underset {j\in {AGTS}}{\bigwedge }}K_{j}\phi .} Common knowledge. Common knowledge of ϕ {\displaystyle \phi } means that everybody knows ϕ {\displaystyle \phi } but also that everybody knows that everybody knows ϕ {\displaystyle \phi } , that everybody knows that everybody knows that everybody knows ϕ {\displaystyle \phi } , and so on ad infinitum. Formally, this corresponds to the following formula C ϕ := E ϕ ∧ E E ϕ ∧ E E E ϕ ∧ … {\displaystyle C\phi :=E\phi \land EE\phi \land EEE\phi \land \ldots } As we do not allow infinite conjunction the notion of common knowledge will have to be introduced as a primitive in our language. Before defining the language with this new operator, we are going to give an example introduced by Lewis that illustrates the difference between the notions of general knowledge and common knowledge. Lewis wanted to know what kind of knowledge is needed so that the statement p {\displaystyle p} : “every driver must drive on the right” be a convention among a group of agents. In other words, he wanted to know what kind of knowledge is needed so that everybody feels safe to drive on the right. Suppose there are only two agents i {\displaystyle i} and j {\displaystyle j} . Then everybody knowing p {\displaystyle p} (formally E p {\displaystyle Ep} ) is not enough. Indeed, it might still be possible that the agent i {\displaystyle i} considers possible that the agent j {\displaystyle j} does not know p {\displaystyle p} (formally ¬ K i K j p {\displaystyle \neg K_{i}K_{j}p} ). In that case the agent i {\displaystyle i} will not feel safe to drive on the right because he might consider that the agent j {\displaystyle j} , not knowing p {\displaystyle p} , could drive on the left. To avoid this problem, we could then assume that everybody knows that everybody knows that p {\displaystyle p} (formally E E p {\displaystyle EEp} ). This is again not enough to ensure that everybody feels safe to drive on the right. Indeed, it might still be possible that agent i {\displaystyle i} considers possible that agent j {\displaystyle j} considers possible that agent i {\displaystyle i} does not know p {\displaystyle p} (formally ¬ K i K j K i p {\displaystyle \neg K_{i}K_{j}K_{i}p} ). In that case and from i {\displaystyle i} ’s point of view, j {\displaystyle j} considers possible that i {\displaystyle i} , not knowing p {\displaystyle p} , will drive on the left. So from i {\displaystyle i} ’s point of view, j {\displaystyle j} might drive on the left as well (by the same argument as abov
Statistical relational learning
Statistical relational learning (SRL) is a subdiscipline of artificial intelligence and machine learning that is concerned with domain models that exhibit both uncertainty (which can be dealt with using statistical methods) and complex, relational structure. Typically, the knowledge representation formalisms developed in SRL use (a subset of) first-order logic to describe relational properties of a domain in a general manner (universal quantification) and draw upon probabilistic graphical models (such as Bayesian networks or Markov networks) to model the uncertainty; some also build upon the methods of inductive logic programming. Significant contributions to the field have been made since the late 1990s. As is evident from the characterization above, the field is not strictly limited to learning aspects; it is equally concerned with reasoning (specifically probabilistic inference) and knowledge representation. Therefore, alternative terms that reflect the main foci of the field include statistical relational learning and reasoning (emphasizing the importance of reasoning) and first-order probabilistic languages (emphasizing the key properties of the languages with which models are represented). Another term that is sometimes used in the literature is relational machine learning (RML). == Canonical tasks == A number of canonical tasks are associated with statistical relational learning, the most common ones being. collective classification, i.e. the (simultaneous) prediction of the class of several objects given objects' attributes and their relations link prediction, i.e. predicting whether or not two or more objects are related link-based clustering, i.e. the grouping of similar objects, where similarity is determined according to the links of an object, and the related task of collaborative filtering, i.e. the filtering for information that is relevant to an entity (where a piece of information is considered relevant to an entity if it is known to be relevant to a similar entity) social network modelling object identification/entity resolution/record linkage, i.e. the identification of equivalent entries in two or more separate databases/datasets == Representation formalisms == One of the fundamental design goals of the representation formalisms developed in SRL is to abstract away from concrete entities and to represent instead general principles that are intended to be universally applicable. Since there are countless ways in which such principles can be represented, many representation formalisms have been proposed in recent years. In the following, some of the more common ones are listed in alphabetical order: Bayesian logic program BLOG model Markov logic networks Multi-entity Bayesian network Probabilistic logic programs Probabilistic relational model – a Probabilistic Relational Model (PRM) is the counterpart of a Bayesian network in statistical relational learning. Probabilistic soft logic Recursive random field Relational Bayesian network Relational dependency network Relational Markov network Relational Kalman filtering
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.
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.