Deepti Gurdasani is a British-Indian clinical epidemiologist and statistical geneticist who is a senior lecturer in machine learning at the Queen Mary University of London. Her research considers the genetic diversity of African Populations. Throughout the COVID-19 pandemic, Gurdasani has provided the public with her analysis of the evolving situation mainly on the Twitter platform. == Early life and education == Gurdasani was an undergraduate and medical student at the Christian Medical College Vellore at Tamil Nadu Dr. M.G.R. Medical University. After earning her medical degree and qualifying in internal medicine, she moved to the United Kingdom, where she worked toward a research doctorate in genetic epidemiology at Wolfson College, Cambridge. Her doctoral research involved the design of strategies to understand complex diseases in diverse populations. == Research and career == In 2013, Gurdasani joined the Wellcome Sanger Institute as a postdoctoral fellow, where she worked on the genomic diversity of African populations and how this diversity impacts susceptibility to disease. She makes use of dense genotypes and whole genome sequences to better understand how population movements determined genetic structure. In particular, Gurdasani develops machine learning algorithms to large-scale clinical data sets. At the Sanger Gurdasani co-led the African Genome Variation Project and the Uganda Resource Project. Gurdasani moved to Queen Mary University of London in 2019, where she created deep learning approaches for clinical prediction and the identification of novel, genome-based drug targets. During the COVID-19 pandemic Gurdasani has provided public commentary on the pandemic, making use of both Twitter and print media to share information on the evolving situation. She has researched the incidence of long covid in the UK. In 2021 Gurdasani started to write for The Guardian. == Selected publications == Deepti Gurdasani; Tommy Carstensen; Fasil Tekola-Ayele; et al. (3 December 2014). "The African Genome Variation Project shapes medical genetics in Africa". Nature. 517 (7534): 327–332. doi:10.1038/NATURE13997. ISSN 1476-4687. PMC 4297536. PMID 25470054. Wikidata Q34979569. Nisreen A Alwan; Rochelle Ann Burgess; Simon Ashworth; et al. (15 October 2020). "Scientific consensus on the COVID-19 pandemic: we need to act now". The Lancet. doi:10.1016/S0140-6736(20)32153-X. ISSN 0140-6736. PMC 7557300. PMID 33069277. Wikidata Q100697134. Deepti Gurdasani; Inês Barroso; Eleftheria Zeggini; Manjinder S Sandhu (24 June 2019). "Genomics of disease risk in globally diverse populations". Nature Reviews Genetics. 20 (9): 520–535. doi:10.1038/S41576-019-0144-0. ISSN 1471-0056. PMID 31235872. Wikidata Q93000887. (erratum)
NetOwl
NetOwl is a suite of multilingual text and identity analytics products that analyze big data in the form of text data – reports, web, social media, etc. – as well as structured entity data about people, organizations, places, and things. NetOwl utilizes artificial intelligence (AI)-based approaches, including natural language processing (NLP), machine learning (ML), and computational linguistics, to extract entities, relationships, and events; to perform sentiment analysis; to assign latitude/longitude to geographical references in text; to translate names written in foreign languages; and to perform name matching and identity resolution. NetOwl's uses include semantic search and discovery, geospatial analysis, intelligence analysis, content enrichment, compliance monitoring, cyber threat monitoring, risk management, and bioinformatics. == History == The first NetOwl product was NetOwl Extractor, which was initially released in 1996. Since then, Extractor has added many new capabilities, including relationship and event extraction, categorization, name translation, geotagging, and sentiment analysis, as well as entity extraction in other languages. Other products were added later to the NetOwl suite, namely TextMiner, NameMatcher, and EntityMatcher. NetOwl has participated in several 3rd party-sponsored text and entity analytics software benchmarking events. NetOwl Extractor was the top-scoring named entity extraction system at the DARPA-sponsored Message Understanding Conference MUC-6 and the top-scoring link and event extraction system in MUC-7. It was also the top-scoring system at several of the NIST-sponsored Automatic Content Extraction (ACE) evaluation tasks. NetOwl NameMatcher was the top-scoring system at the MITRE Challenge for Multicultural Person Name Matching. == Products == The NetOwl suite includes, among others, the following text and entity analytics products: === Text Analytics === NetOwl Extractor performs entity extraction from unstructured texts using natural language processing (NLP), machine learning (ML), and computational linguistics. Extractor also performs semantic relationship and event extraction as well as geotagging of text. It is used for a variety of data sources including both traditional sources (e.g., news, reports, web pages, email) and social media (e.g., Twitter, Facebook, chats, blogs). It runs on a variety of Big Data analytics platforms, including Apache Hadoop and LexisNexis’s High-Performance Computer Cluster (HPCC) technology. It has been integrated with a number of 3rd party analytical tools such as Esri ArcGIS and Google Earth/Maps. === Identity Analytics === NetOwl NameMatcher and EntityMatcher perform name matching and identity resolution for large multicultural and multilingual entity databases using machine learning (ML) and computational linguistics approaches. They are used for applications such as anti–money laundering (AML), watch lists, regulatory compliance, fraud detection, etc.
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'.
Variable kernel density estimation
In statistics, adaptive or "variable-bandwidth" kernel density estimation is a form of kernel density estimation in which the size of the kernels used in the estimate are varied depending upon either the location of the samples or the location of the test point. It is a particularly effective technique when the sample space is multi-dimensional. == Rationale == Given a set of samples, { x → i } {\displaystyle \lbrace {\vec {x}}_{i}\rbrace } , we wish to estimate the density, P ( x → ) {\displaystyle P({\vec {x}})} , at a test point, x → {\displaystyle {\vec {x}}} : P ( x → ) ≈ W n h D {\displaystyle P({\vec {x}})\approx {\frac {W}{nh^{D}}}} W = ∑ i = 1 n w i {\displaystyle W=\sum _{i=1}^{n}w_{i}} w i = K ( x → − x → i h ) {\displaystyle w_{i}=K\left({\frac {{\vec {x}}-{\vec {x}}_{i}}{h}}\right)} where n is the number of samples, K is the "kernel", h is its width and D is the number of dimensions in x → {\displaystyle {\vec {x}}} . The kernel can be thought of as a simple, linear filter. Using a fixed filter width may mean that in regions of low density, all samples will fall in the tails of the filter with very low weighting, while regions of high density will find an excessive number of samples in the central region with weighting close to unity. To fix this problem, we vary the width of the kernel in different regions of the sample space. There are two methods of doing this: balloon and pointwise estimation. In a balloon estimator, the kernel width is varied depending on the location of the test point. In a pointwise estimator, the kernel width is varied depending on the location of the sample. For multivariate estimators, the parameter, h, can be generalized to vary not just the size, but also the shape of the kernel. This more complicated approach will not be covered here. == Balloon estimators == A common method of varying the kernel width is to make it inversely proportional to the density at the test point: h = k [ n P ( x → ) ] 1 / D {\displaystyle h={\frac {k}{\left[nP({\vec {x}})\right]^{1/D}}}} where k is a constant. If we back-substitute the estimated PDF, and assuming a Gaussian kernel function, we can show that W is a constant: W = k D ( 2 π ) D / 2 {\displaystyle W=k^{D}(2\pi )^{D/2}} A similar derivation holds for any kernel whose normalising function is of the order hD, although with a different constant factor in place of the (2 π)D/2 term. This produces a generalization of the k-nearest neighbour algorithm. That is, a uniform kernel function will return the KNN technique. There are two components to the error: a variance term and a bias term. The variance term is given as: e 1 = P ∫ K 2 n h D {\displaystyle e_{1}={\frac {P\int K^{2}}{nh^{D}}}} . The bias term is found by evaluating the approximated function in the limit as the kernel width becomes much larger than the sample spacing. By using a Taylor expansion for the real function, the bias term drops out: e 2 = h 2 n ∇ 2 P {\displaystyle e_{2}={\frac {h^{2}}{n}}\nabla ^{2}P} An optimal kernel width that minimizes the error of each estimate can thus be derived. == Use for statistical classification == The method is particularly effective when applied to statistical classification. There are two ways we can proceed: the first is to compute the PDFs of each class separately, using different bandwidth parameters, and then compare them as in Taylor. Alternatively, we can divide up the sum based on the class of each sample: P ( j , x → ) ≈ 1 n ∑ i = 1 , c i = j n w i {\displaystyle P(j,{\vec {x}})\approx {\frac {1}{n}}\sum _{i=1,c_{i}=j}^{n}w_{i}} where ci is the class of the ith sample. The class of the test point may be estimated through maximum likelihood.
Recursive neural network
A recursive neural network is a kind of deep neural network created by applying the same set of weights recursively over a structured input, to produce a structured prediction over variable-size input structures, or a scalar prediction on it, by traversing a given structure in topological order. These networks were first introduced to learn distributed representations of structure (such as logical terms), but have been successful in multiple applications, for instance in learning sequence and tree structures in natural language processing (mainly continuous representations of phrases and sentences based on word embeddings). == Architectures == === Basic === In the simplest architecture, nodes are combined into parents using a weight matrix (which is shared across the whole network) and a non-linearity such as the tanh {\displaystyle \tanh } hyperbolic function. If c 1 {\displaystyle c_{1}} and c 2 {\displaystyle c_{2}} are n {\displaystyle n} -dimensional vector representations of nodes, their parent will also be an n {\displaystyle n} -dimensional vector, defined as: p 1 , 2 = tanh ( W [ c 1 ; c 2 ] ) {\displaystyle p_{1,2}=\tanh(W[c_{1};c_{2}])} where W {\displaystyle W} is a learned n × 2 n {\displaystyle n\times 2n} weight matrix. This architecture, with a few improvements, has been used for successfully parsing natural scenes, syntactic parsing of natural language sentences, and recursive autoencoding and generative modeling of 3D shape structures in the form of cuboid abstractions. === Recursive cascade correlation (RecCC) === RecCC is a constructive neural network approach to deal with tree domains with pioneering applications to chemistry and extension to directed acyclic graphs. === Unsupervised RNN === A framework for unsupervised RNN has been introduced in 2004. === Tensor === Recursive neural tensor networks use a single tensor-based composition function for all nodes in the tree. == Training == === Stochastic gradient descent === Typically, stochastic gradient descent (SGD) is used to train the network. The gradient is computed using backpropagation through structure (BPTS), a variant of backpropagation through time used for recurrent neural networks. == Properties == The universal approximation capability of RNNs over trees has been proved in literature. == Related models == === Recurrent neural networks === Recurrent neural networks are recursive artificial neural networks with a certain structure: that of a linear chain. Whereas recursive neural networks operate on any hierarchical structure, combining child representations into parent representations, recurrent neural networks operate on the linear progression of time, combining the previous time step and a hidden representation into the representation for the current time step. === Tree Echo State Networks === An efficient approach to implement recursive neural networks is given by the Tree Echo State Network within the reservoir computing paradigm. === Extension to graphs === Extensions to graphs include graph neural network (GNN), Neural Network for Graphs (NN4G), and more recently convolutional neural networks for graphs.
SWIG
The Simplified Wrapper and Interface Generator (SWIG) is an open-source software tool used to connect computer programs or libraries written in C or C++ with scripting languages such as Lua, Perl, PHP, Python, R, Ruby, Tcl, and other language implementations like C#, Java, JavaScript, Go, D, OCaml, Octave, Scilab and Scheme. Output can also be in the form of XML. == Function == The aim is to allow the calling of native functions (that were written in C or C++) by other programming languages, passing complex data types to those functions, keeping memory from being inappropriately freed, inheriting object classes across languages, etc. The programmer writes an interface file containing a list of C/C++ functions to be made visible to an interpreter. SWIG will compile the interface file and generate code in regular C/C++ and the target programming language. SWIG will generate conversion code for functions with simple arguments; conversion code for complex types of arguments must be written by the programmer. The SWIG tool creates source code that provides the glue between C/C++ and the target language. Depending on the language, this glue comes in three forms: a shared library that an extant interpreter can link to as some form of extension module, or a shared library that can be linked to other programs compiled in the target language (for example, using Java Native Interface (JNI) in Java). a shared dynamic library source code that should be compiled and dynamically loaded (e.g. Node.js native extensions) SWIG is not used for calling interpreted functions by native code; this must be done by the programmer manually. == Example == SWIG wraps simple C declarations by creating an interface that closely matches the way in which the declarations would be used in a C program. For example, consider the following interface file: In this file, there are two functions sin() and strcmp(), a global variable Foo, and two constants STATUS and VERSION. When SWIG creates an extension module, these declarations are accessible as scripting language functions, variables, and constants respectively. In Python: == Purpose == There are two main reasons to embed a scripting engine in an existing C/C++ program: The program can then be customized far faster, via a scripting language instead of C/C++. The scripting engine may even be exposed to the end-user, so that they can automate common tasks by writing scripts. Even if the final product is not to contain the scripting engine, it may nevertheless be very useful for writing test scripts. There are several reasons to create dynamic libraries that can be loaded into extant interpreters, including: Provide access to a C/C++ library which has no equivalent in the scripting language. Write the whole program in the scripting language first, and after profiling, rewrite performance-critical code in C or C++. == History == SWIG is written in C and C++ and has been publicly available since February 1996. The initial author and main developer was David M. Beazley who developed SWIG while working as a graduate student at Los Alamos National Laboratory and the University of Utah and while on the faculty at the University of Chicago. Development is currently supported by an active group of volunteers led by William Fulton. SWIG has been released under a GNU General Public License. == Google Summer of Code == SWIG was a successful participant of Google Summer of Code in 2008, 2009, 2012. In 2008, SWIG got four slots. Haoyu Bai spent his summers on SWIG's Python 3.0 Backend, Jan Jezabek worked on Support for generating COM wrappers, Cheryl Foil spent her time on Comment 'Translator' for SWIG, and Maciej Drwal worked on a C backend. In 2009, SWIG again participated in Google Summer of Code. This time four students participated. Baozeng Ding worked on a Scilab module. Matevz Jekovec spent time on C++0x features. Ashish Sharma spent his summer on an Objective-C module, Miklos Vajna spent his time on PHP directors. In 2012, SWIG participated in Google Summer of Code. This time four out of five students successfully completed the project. Leif Middelschulte worked on a C target language module. Swati Sharma enhanced the Objective-C module. Neha Narang added the new module on JavaScript. Dmitry Kabak worked on source code documentation and Doxygen comments. == Alternatives == For Python, similar functionality is offered by SIP, Pybind11, and Boost's Boost.python library. == Projects using SWIG == ZXID (Apache License, Version 2.0) Symlabs SFIS (commercial) LLDB GNU Radio up to (including) version 3.8.x.x; later versions use Pybind11 Xapian TensorFlow Apache SINGA QuantLib Babeltrace
Vladimir Batagelj
Vladimir Batagelj (born June 14, 1948 in Idrija, Yugoslavia) is a Slovenian mathematician and an emeritus professor of mathematics at the University of Ljubljana. He is known for his work in discrete mathematics and combinatorial optimization, particularly analysis of social networks and other large networks (blockmodeling). == Education and career == Vladimir Batagelj completed his Ph.D. at the University of Ljubljana in 1986 under the direction of Tomaž Pisanski. He stayed at the University of Ljubljana as a professor until his retirement, where he was a professor of sociology and statistics, while also being a chair of the Department of Sociology of the Faculty of Social Sciences. As visiting professor, he was taught at the University of Pittsburgh (1990-91) and at the University of Konstanz (2002). He was also a member of editorial boards of two journals: Informatica and Journal of Social Structure. His work has been cited over 11000 times. His book Exploratory Social Network Analysis with Pajek on blockmodeling, coauthored with Wouter de Nooy and Andrej Mrvar, is Batagelj's most cited work and has over 3300 citations. The book was translated into Chinese and Japanese. The revised and expanded third edition has been published by Cambridge University Press. In 1975, 11 years before completing his PhD, Batagelj published a solo paper in Communications of the ACM. Batagelj authored more than 20 textbooks in Slovenian, covering topics like TeX, combinatorics and discrete mathematics. He has also written extensively in the Slovenian popular science journal Presek. Batagelj has advised 9 Ph.D. students. == Pajek == Batagelj is particularly known for his work on Pajek, a freely available software for analysis and visualization of large networks. He began work on Pajek in 1996 with Andrej Mrvar, who was then his PhD student. == Awards and honors == First prizes for contributions (with Andrej Mrvar) to Graph Drawing Contests in years: 1995, 1996, 1997, 1998, 1999, 2000 and 2005 / Graph Drawing Hall of Fame. In 2007 the book Generalized blockmodeling was awarded the Harrison White Outstanding Book Award by the Mathematical Sociology Section of American Sociological Association In 2007 he was awarded (together with Anuška Ferligoj) the Simmel Award by INSNA. In 2013, Vladimir Batagelj and Andrej Mrvar received the INSNA's William D. Richards Software award for their work on Pajek. == Selected bibliography == Vladimir Batagelj, Social Network Analysis, Large-Scale [1]. in R.A. Meyers, ed., Encyclopedia of Complexity and Systems Science, Springer 2009: 8245–8265. Vladimir Batagelj, Complex Networks, Visualization of [2]. in R.A. Meyers, ed., Encyclopedia of Complexity and Systems Science, Springer 2009: 1253–1268. Wouter de Nooy, Andrej Mrvar, Vladimir Batagelj, Mark Granovetter (Series Editor), Exploratory Social Network Analysis with Pajek (Structural Analysis in the Social Sciences), Cambridge University Press 2005 (ISBN 0-521-60262-9). ESNA in Japanese, TDU, 2010. Patrick Doreian, Vladimir Batagelj, Anuška Ferligoj, Mark Granovetter (Series Editor), Generalized Blockmodeling (Structural Analysis in the Social Sciences), Cambridge University Press 2004 (ISBN 0-521-84085-6)