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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.
Jubatus
Jubatus is an open-source online machine learning and distributed computing framework developed at Nippon Telegraph and Telephone and Preferred Infrastructure. Its features include classification, recommendation, regression, anomaly detection and graph mining. It supports many client languages, including C++, Java, Ruby and Python. It uses Iterative Parameter Mixture for distributed machine learning. == Notable Features == Jubatus supports: Multi-classification algorithms: Perceptron Passive Aggressive Confidence Weighted Adaptive Regularization of Weight Vectors Normal Herd Recommendation algorithms using: Inverted index Minhash Locality-sensitive hashing Regression algorithms: Passive Aggressive feature extraction method for natural language: n-gram Text segmentation
Physical neural network
A physical neural network is a type of artificial neural network in which an electrically adjustable material is used to emulate the function of a neural synapse or a higher-order (dendritic) neuron model. "Physical" neural network is used to emphasize the reliance on physical hardware used to emulate neurons as opposed to software-based approaches. More generally the term is applicable to other artificial neural networks in which a memristor or other electrically adjustable resistance material is used to emulate a neural synapse. == Types of physical neural networks == === ADALINE === In the 1960s Bernard Widrow and Ted Hoff developed ADALINE (Adaptive Linear Neuron) which used electrochemical cells called memistors (memory resistors) to emulate synapses of an artificial neuron. The memistors were implemented as 3-terminal devices operating based on the reversible electroplating of copper such that the resistance between two of the terminals is controlled by the integral of the current applied via the third terminal. The ADALINE circuitry was briefly commercialized by the Memistor Corporation in the 1960s enabling some applications in pattern recognition. However, since the memistors were not fabricated using integrated circuit fabrication techniques the technology was not scalable and was eventually abandoned as solid-state electronics became mature. === Analog VLSI === In 1989 Carver Mead published his book Analog VLSI and Neural Systems, which spun off perhaps the most common variant of analog neural networks. The physical realization is implemented in analog VLSI. This is often implemented as field effect transistors in low inversion. Such devices can be modelled as translinear circuits. This is a technique described by Barrie Gilbert in several papers around mid 1970th, and in particular his Translinear Circuits from 1981. With this method circuits can be analyzed as a set of well-defined functions in steady-state, and such circuits assembled into complex networks. === Physical Neural Network === Alex Nugent describes a physical neural network as one or more nonlinear neuron-like nodes used to sum signals and nanoconnections formed from nanoparticles, nanowires, or nanotubes which determine the signal strength input to the nodes. Alignment or self-assembly of the nanoconnections is determined by the history of the applied electric field performing a function analogous to neural synapses. Numerous applications for such physical neural networks are possible. For example, a temporal summation device can be composed of one or more nanoconnections having an input and an output thereof, wherein an input signal provided to the input causes one or more of the nanoconnection to experience an increase in connection strength thereof over time. Another example of a physical neural network is taught by U.S. Patent No. 7,039,619 entitled "Utilized nanotechnology apparatus using a neural network, a solution and a connection gap," which issued to Alex Nugent by the U.S. Patent & Trademark Office on May 2, 2006. A further application of physical neural network is shown in U.S. Patent No. 7,412,428 entitled "Application of hebbian and anti-hebbian learning to nanotechnology-based physical neural networks," which issued on August 12, 2008. Nugent and Molter have shown that universal computing and general-purpose machine learning are possible from operations available through simple memristive circuits operating the AHaH plasticity rule. More recently, it has been argued that also complex networks of purely memristive circuits can serve as neural networks. === Phase change neural network === In 2002, Stanford Ovshinsky described an analog neural computing medium in which phase-change material has the ability to cumulatively respond to multiple input signals. An electrical alteration of the resistance of the phase change material is used to control the weighting of the input signals. === Memristive neural network === Greg Snider of HP Labs describes a system of cortical computing with memristive nanodevices. The memristors (memory resistors) are implemented by thin film materials in which the resistance is electrically tuned via the transport of ions or oxygen vacancies within the film. DARPA's SyNAPSE project has funded IBM Research and HP Labs, in collaboration with the Boston University Department of Cognitive and Neural Systems (CNS), to develop neuromorphic architectures which may be based on memristive systems. === Protonic artificial synapses === In 2022, researchers reported the development of nanoscale brain-inspired artificial synapses, using the ion proton (H+), for 'analog deep learning'.
Perceptron
In machine learning, the perceptron is an algorithm for supervised learning of binary classifiers. A binary classifier is a function that can decide whether or not an input, represented by a vector of numbers, belongs to some specific class. It is a type of linear classifier, i.e. a classification algorithm that makes its predictions based on a linear predictor function combining a set of weights with the feature vector. == History == The artificial neuron and artificial neural network were invented in 1943 by Warren McCulloch and Walter Pitts in their seminal paper "A Logical Calculus of the Ideas Immanent in Nervous Activity". In 1957, Frank Rosenblatt was at the Cornell Aeronautical Laboratory. He simulated the perceptron on an IBM 704. Later, he obtained funding by the Information Systems Branch of the United States Office of Naval Research and the Rome Air Development Center, to build a custom-made computer, the Mark I Perceptron. It was first publicly demonstrated on 23 June 1960. The machine was "part of a previously secret four-year NPIC [the US' National Photographic Interpretation Center] effort from 1963 through 1966 to develop this algorithm into a useful tool for photo-interpreters". Rosenblatt described the details of the perceptron in a 1958 paper. His organization of a perceptron is constructed of three kinds of cells ("units"): S, A, R, which stand for "sensory", "association" and "response". He presented at the first international symposium on AI, Mechanisation of Thought Processes, which took place in 1958 November. Rosenblatt's project was funded under Contract Nonr-401(40) "Cognitive Systems Research Program", which lasted from 1959 to 1970, and Contract Nonr-2381(00) "Project PARA" ("PARA" means "Perceiving and Recognition Automata"), which lasted from 1957 to 1963. In 1959, the Institute for Defense Analysis awarded his group a $10,000 contract. By September 1961, the ONR awarded further $153,000 worth of contracts, with $108,000 committed for 1962. The ONR research manager, Marvin Denicoff, stated that ONR, instead of ARPA, funded the Perceptron project, because the project was unlikely to produce technological results in the near or medium term. Funding from ARPA go up to the order of millions dollars, while from ONR are on the order of 10,000 dollars. Meanwhile, the head of IPTO at ARPA, J.C.R. Licklider, was interested in 'self-organizing', 'adaptive' and other biologically-inspired methods in the 1950s; but by the mid-1960s he was openly critical of these, including the perceptron. Instead he strongly favored the logical AI approach of Simon and Newell. === Mark I Perceptron machine === The perceptron was intended to be a machine, rather than a program, and while its first implementation was in software for the IBM 704, it was subsequently implemented in custom-built hardware as the Mark I Perceptron with the project name "Project PARA", designed for image recognition. The machine is currently in Smithsonian National Museum of American History. The Mark I Perceptron had three layers. One version was implemented as follows: An array of 400 photocells arranged in a 20x20 grid, named "sensory units" (S-units), or "input retina". Each S-unit can connect to up to 40 A-units. A hidden layer of 512 perceptrons, named "association units" (A-units). An output layer of eight perceptrons, named "response units" (R-units). Rosenblatt called this three-layered perceptron network the alpha-perceptron, to distinguish it from other perceptron models he experimented with. The S-units are connected to the A-units randomly (according to a table of random numbers) via a plugboard (see photo), to "eliminate any particular intentional bias in the perceptron". The connection weights are fixed, not learned. Rosenblatt was adamant about the random connections, as he believed the retina was randomly connected to the visual cortex, and he wanted his perceptron machine to resemble human visual perception. The A-units are connected to the R-units, with adjustable weights encoded in potentiometers, and weight updates during learning were performed by electric motors.The hardware details are in an operators' manual. In a 1958 press conference organized by the US Navy, Rosenblatt made statements about the perceptron that caused a heated controversy among the fledgling AI community; based on Rosenblatt's statements, The New York Times reported the perceptron to be "the embryo of an electronic computer that [the Navy] expects will be able to walk, talk, see, write, reproduce itself and be conscious of its existence." The Photo Division of Central Intelligence Agency, from 1960 to 1964, studied the use of Mark I Perceptron machine for recognizing militarily interesting silhouetted targets (such as planes and ships) in aerial photos. === Principles of Neurodynamics (1962) === Rosenblatt described his experiments with many variants of the Perceptron machine in a book Principles of Neurodynamics (1962). The book is a published version of the 1961 report. Among the variants are: "cross-coupling" (connections between units within the same layer) with possibly closed loops, "back-coupling" (connections from units in a later layer to units in a previous layer), four-layer perceptrons where the last two layers have adjustable weights (and thus a proper multilayer perceptron), incorporating time-delays to perceptron units, to allow for processing sequential data, analyzing audio (instead of images). The machine was shipped from Cornell to Smithsonian in 1967, under a government transfer administered by the Office of Naval Research. === Perceptrons (1969) === Although the perceptron initially seemed promising, it was quickly proved that perceptrons could not be trained to recognise many classes of patterns. This caused the field of neural network research to stagnate for many years, before it was recognised that a feedforward neural network with two or more layers (also called a multilayer perceptron) had greater processing power than perceptrons with one layer (also called a single-layer perceptron). Single-layer perceptrons are only capable of learning linearly separable patterns. For a classification task with some step activation function, a single node will have a single line dividing the data points forming the patterns. More nodes can create more dividing lines, but those lines must somehow be combined to form more complex classifications. A second layer of perceptrons, or even linear nodes, are sufficient to solve many otherwise non-separable problems. In 1969, a famous book entitled Perceptrons by Marvin Minsky and Seymour Papert showed that it was impossible for these classes of network to learn an XOR function. It is often incorrectly believed that they also conjectured that a similar result would hold for a multi-layer perceptron network. However, this is not true, as both Minsky and Papert already knew that multi-layer perceptrons were capable of producing an XOR function. (See the page on Perceptrons (book) for more information.) Nevertheless, the often-miscited Minsky and Papert text caused a significant decline in interest and funding of neural network research. It took ten more years until neural network research experienced a resurgence in the 1980s. This text was reprinted in 1987 as "Perceptrons - Expanded Edition" where some errors in the original text are shown and corrected. === Subsequent work === Rosenblatt continued working on perceptrons despite diminishing funding. The last attempt was Tobermory, built between 1961 and 1967, built for speech recognition. It occupied an entire room. It had 4 layers with 12,000 weights implemented by toroidal magnetic cores. By the time of its completion, simulation on digital computers had become faster than purpose-built perceptron machines. He died in a boating accident in 1971. A simulation program for neural networks was written for IBM 7090/7094, and was used to study various pattern recognition applications, such as character recognition, particle tracks in bubble-chamber photographs; phoneme, isolated word, and continuous speech recognition; speaker verification; and center-of-attention mechanisms for image processing. The kernel perceptron algorithm was already introduced in 1964 by Aizerman et al. Margin bounds guarantees were given for the Perceptron algorithm in the general non-separable case first by Freund and Schapire (1998), and more recently by Mohri and Rostamizadeh (2013) who extend previous results and give new and more favorable L1 bounds. The perceptron is a simplified model of a biological neuron. While the complexity of biological neuron models is often required to fully understand neural behavior, research suggests a perceptron-like linear model can produce some behavior seen in real neurons. The solution spaces of decision boundaries for all binary functions and learning behaviors are studied in. == Definition == In the modern sense, the perceptron is an algori
Hybrid intelligent system
Hybrid intelligent system denotes a software system which employs, in parallel, a combination of methods and techniques from artificial intelligence subfields, such as: Neuro-symbolic systems Neuro-fuzzy systems Hybrid connectionist-symbolic models Fuzzy expert systems Connectionist expert systems Evolutionary neural networks Genetic fuzzy systems Rough fuzzy hybridization Reinforcement learning with fuzzy, neural, or evolutionary methods as well as symbolic reasoning methods. From the cognitive science perspective, every natural intelligent system is hybrid because it performs mental operations on both the symbolic and subsymbolic levels. For the past few years, there has been an increasing discussion of the importance of A.I. Systems Integration. Based on notions that there have already been created simple and specific AI systems (such as systems for computer vision, speech synthesis, etc., or software that employs some of the models mentioned above) and now is the time for integration to create broad AI systems. Proponents of this approach are researchers such as Marvin Minsky, Ron Sun, Aaron Sloman, Angelo Dalli and Michael A. Arbib. An example hybrid is a hierarchical control system in which the lowest, reactive layers are sub-symbolic. The higher layers, having relaxed time constraints, are capable of reasoning from an abstract world model and performing planning (even by hybrid wisdom). Intelligent systems usually rely on hybrid reasoning processes, which include induction, deduction, abduction and reasoning by analogy.
Generalized blockmodeling
In generalized blockmodeling, the blockmodeling is done by "the translation of an equivalence type into a set of permitted block types", which differs from the conventional blockmodeling, which is using the indirect approach. It's a special instance of the direct blockmodeling approach. Generalized blockmodeling was introduced in 1994 by Patrick Doreian, Vladimir Batagelj and Anuška Ferligoj. == Definition == Generalized blockmodeling approach is a direct one, "where the optimal partition(s) is (are) identified based on minimal values of a compatible criterion function defined by the difference between empirical blocks and corresponding ideal blocks". At the same time, the much broader set of block types is introduced (while in conventional blockmodeling only certain types are used). The conventional blockmodeling is inductive due to nonspecification of neither the clusters or the location of block types, while in generalized blockmodeling the blockmodel is specified with more detail than just the permition of certain block types (e.g., prespecification). Further, it's possible to define departures from the permitted (ideal) blocktype, using criterion function. Using local optimization procedure, firstly the initial clustering (with specified number of clusters is done, based on random creation. How the clusters are neighboring to each other, is based on two transformations: 1) a vertex is moved from one to another cluster or 2) a pair of vertices is interchanged between two different clusters. This process of transformation steps is repeated many times, until only the best fitting partitions (with the minimized value of the criterion function) are kept as blockmodels for the future exploration of the network. Different types of generalized blockmodeling are: generalized binary blockmodeling, generalized valued blockmodeling and generalized homogeneity blockmodeling. == Benefits == According to Patrick Doreian, the benefits of generalized blockmodeling, are as follows: usage of explicit criterion function, compatible with a given type of equivalence, results to in-built measure of fit, which is integral to the establishment of the blockmodels (in conventional blockmodeling, there is no compelling and coherent measures of fit); partitions, based on generalized blockmodeling, regularly outperform and never perform less well than the partitions, based on conventional approach; with generalized blockmodeling it's possible to specify new types of blockmodels; this potentially unlimited set of new block types also results in permittion of inclusion of substantively driven blockmodels; in generalized blockmodeling, the specification of the block types and the location of some of them in the blockmodel is possible; researcher can speficy which (pair of) vertices must be (not) clustered together; this approach also allows the imposition of penalties, resulting into identification of empirical null blocks without inconsistencies with a corresponding ideal null block. == Problems == According to Doreian, the problems of generalized blockmodeling, are as follows: unknown sensitivity to particular data features, examination of boundary problems, computationally burdensome, which results in a constraint regarding practical network size (generalized blockmodeling is thus primarily used to analyse smaller networks (below 100 units)), identifying structure from incomplete network information, most of generalized blockmodeling is based on binary networks, but there is also development in the field of valued networks, criterion function is minimized for a specified blockmodel, with results in issues of evaluating statistically, based on the structural data alone, problems regarding three dimensional network data, problems regarding the evolution of fundamental network structure. == Book == The book with the same title, Generalized blockmodeling, written by Patrick Doreian, Vladimir Batagelj and Anuška Ferligoj, was in 2007 awarded the Harrison White Outstanding Book Award by the Mathematical Sociology Section of American Sociological Association.