Elastix is an image registration toolbox built upon the Insight Segmentation and Registration Toolkit (ITK). It is entirely open-source and provides a wide range of algorithms employed in image registration problems. Its components are designed to be modular to ease a fast and reliable creation of various registration pipelines tailored for case-specific applications. It was first developed by Stefan Klein and Marius Staring under the supervision of Josien P.W. Pluim at Image Sciences Institute (ISI). Its first version was command-line based, allowing the final user to employ scripts to automatically process big data-sets and deploy multiple registration pipelines with few lines of code. Nowadays, to further widen its audience, a version called SimpleElastix is also available, developed by Kasper Marstal, which allows the integration of elastix with high level languages, such as Python, Java, and R. == Image registration fundamentals == Image registration is a well-known technique in digital image processing that searches for the geometric transformation that, applied to a moving image, obtains a one-to-one map with a target image. Generally, the images acquired from different sensors (multimodal), time instants (multitemporal), and points of view (multiview) should be correctly aligned to proceed with further processing and feature extraction. Even though there are a plethora of different approaches to image registration, the majority is composed of the same macro building blocks, namely the transformation, the interpolator, the metric, and the optimizer. Registering two or more images can be framed as an optimization problem that requires multiple iterations to converge to the best solution. Starting from an initial transformation computed from the image moments the optimization process searches for the best transformation parameters based on the value of the selected similarity metric. The figure on the right shows the high-level representation of the registration of two images, where the reference remains constant during the entire process, while the moving one will be transformed according to the transformation parameters. In other words, the registration ends when the similarity metric, which is a mathematical function with a certain number of parameters to be optimized, reaches the optimal value which is highly dependent on the specific application. == Main building blocks == Following the structure of the image registration workflow, the elastix toolbox proposes a modular solution that implements for each of the building blocks different algorithms, highly employed in medical image registration, and helps the final users to build their specific pipeline by selecting the most suitable algorithm for each of the main building blocks. Each block is easily configurable both by selecting pre-defined initialization values or by trying multiple sets of parameters and then choosing the most performing one. The registration is performed on images, and the elastix toolbox supports all the data formats supported by ITK, ranging from JPEG and PNG to medical standard formats such as DICOM and NIFTI. It also stores physical pixel spacing, the origin and the relative position to an external world reference system, when provided in the metadata, to facilitate the registration process, especially in medical field applications. === Transformation === The transformation is an essential building block, since it defines the allowable transformations. In image registration, the main distinction can be done between parallel-to-parallel and parallel-to-non parallel (deformable) line mapping transformations. In the elastix toolbox, the final users can select one transformation or compose more transformations either through addition or via composition. Below are reported the different transformation models in order of increasing flexibility, along with the corresponding elastix class names between brackets. Translation (TranslationTransform) allows only translations Rigid (EulerTransform) expands the translation adding rotations and the object is seen as a rigid body Similarity (SimilarityTransform) expands the rigid transformation by introducing isotropic scaling Affine (AffineTransform) expands the rigid transformation allowing both scaling and shear B-splines (BSplineTransform) is a deformable transformation usually preceded by a rigid or affine one Thin-plate splines (SplineKernelTransform) is a deformable transformation belonging to the class of kernel-based transformations that is a composition of and affine and a non-rigid part === Metric === The similarity metric is the mathematical function whose parameters should be optimized to reach the desired registration, and, during the process, it is computed multiple times. Below are reported the available metrics computed employing the reference and the transformed images and the corresponding elastix class names between brackets. Mean squared difference (AdvancedMeanSquares) to be used for mono-modal applications Normalized correlation coefficient (AdvancedNormalizedCorrelation) to be used for images that have an intensity linear relationship Mutual information (AdvancedMattesMutualInformation) to be used for both mono- and multi-modal applications and optimized to reach better performance compared to the normalized version Normalized mutual information (NormalizedMutualInformation) for both mono- and multi-modal applications Kappa statistic (AdvancedKappaStatistic) to be used only for binary images === Sampler === For the computation of the similarity metrics, it is not always necessary to consider all the voxels and, sometimes, it can be useful to use only a fraction of the voxels of the images, i.e. to reduce the execution time for big input images. Below are reported the available criteria for selecting a fraction of the voxels for the similarity metric computation and the corresponding elastix class names between brackets. Full (Full) to employ all the voxels Grid (Grid) to employ a regular grid defined by the user to downsample the image Random (Random) to randomly select a percentage of voxels defined by the users (all voxels have equal probability to be selected) Random coordinate (RandomCoordinate) like the random criterion, but in this case also off-grid positions can be selected to simplify the optimization process === Interpolator === After the application of the transformation, it may occur that the voxels used for the similarity metric computation are at non-voxel positions, so intensity interpolation should be performed to ensure the correctness of the computed values. Below are reported the implemented interpolators and the corresponding elastix class names between brackets. Nearest neighbor (NearestNeighborInterpolator) exploits little resources, but gives low quality results Linear (LinearInterpolator) is sufficient in general applications N-th order B-spline (BSplineInterpolator) can be used to increase the order N, increasing quality and computation time. N=0 and N=1 indicate the nearest neighbor and linear cases respectively. === Optimizer === The optimizer defines the strategy employed for searching the best transformation parameter to reach the correct registration, and it is commonly an iterative strategy. Below are reported some of the implemented optimization strategies. Gradient descent Robbins-Monro, similar to the gradient descent, but employing an approximation of the cost function derivatives A wider range of optimizers is also available, such as Quasi-Newton or evolutionary strategies. === Other features === The elastix software also offers other features that can be employed to speed up the registration procedure and to provide more advanced algorithms to the end-users. Some examples are the introduction of blur and Gaussian pyramid to reduce data complexity, and multi-image and multi-metric framework to deal with more complex applications. == Applications == Elastix has applications mainly in the medical field, where image registration is fundamental to get comprehensive information regarding the analysed anatomical region. It is widely employed in image-guided surgery, tumour monitoring, and treatment assessment. For example, in radiotherapy planning, image registration allows to correctly deliver the treatment and evaluate the obtained results. Thanks to the wide range of implemented algorithms, the use of the elastix software allows physicians and researchers to test different registration pipelines from the simplest to more complex ones, and to save the best one as a configuration file. This file and the fact that the software is completely open-source makes it easy to reproduce the work, that can help supporting the open science paradigm, and allows fast reuse on different patients data. In image-guided surgery, registration time and accuracy are critical points, considering that, during the registration, the patient is on the operating table, and the imag
Pandorabots
Pandorabots, Inc. is an artificial intelligence company that runs a web service for building and deploying chatbots. Pandorabots implements and supports development of the Artificial Intelligence Markup Language and makes portions of its code accessible for free. The Pandorabots Platform is "one of the oldest and largest chatbot hosting services in the world", allowing creation of virtual agents to hold human-like text or voice chats with consumers. The platform is written in Allegro Common LISP. == Use Cases == Common use cases include advertising, virtual assistance, e-learning, entertainment and education. The platform has also been used by academics and universities use the platform for teaching and research.
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'.
Randomized weighted majority algorithm
The randomized weighted majority algorithm is an algorithm in machine learning theory for aggregating expert predictions to a series of decision problems. It is a simple and effective method based on weighted voting which improves on the mistake bound of the deterministic weighted majority algorithm. In fact, in the limit, its prediction rate can be arbitrarily close to that of the best-predicting expert. == Example == Imagine that every morning before the stock market opens, we get a prediction from each of our "experts" about whether the stock market will go up or down. Our goal is to somehow combine this set of predictions into a single prediction that we then use to make a buy or sell decision for the day. The principal challenge is that we do not know which experts will give better or worse predictions. The RWMA gives us a way to do this combination such that our prediction record will be nearly as good as that of the single expert which, in hindsight, gave the most accurate predictions. == Motivation == In machine learning, the weighted majority algorithm (WMA) is a deterministic meta-learning algorithm for aggregating expert predictions. In pseudocode, the WMA is as follows: initialize all experts to weight 1 for each round: add each expert's weight to the option they predicted predict the option with the largest weighted sum multiply the weights of all experts who predicted wrongly by 1 2 {\displaystyle {\frac {1}{2}}} Suppose there are n {\displaystyle n} experts and the best expert makes m {\displaystyle m} mistakes. Then, the weighted majority algorithm (WMA) makes at most 2.4 ( log 2 n + m ) {\displaystyle 2.4(\log _{2}n+m)} mistakes. This bound is highly problematic in the case of highly error-prone experts. Suppose, for example, the best expert makes a mistake 20% of the time; that is, in N = 100 {\displaystyle N=100} rounds using n = 10 {\displaystyle n=10} experts, the best expert makes m = 20 {\displaystyle m=20} mistakes. Then, the weighted majority algorithm only guarantees an upper bound of 2.4 ( log 2 10 + 20 ) ≈ 56 {\displaystyle 2.4(\log _{2}10+20)\approx 56} mistakes. As this is a known limitation of the weighted majority algorithm, various strategies have been explored in order to improve the dependence on m {\displaystyle m} . In particular, we can do better by introducing randomization. Drawing inspiration from the Multiplicative Weights Update Method algorithm, we will probabilistically make predictions based on how the experts have performed in the past. Similarly to the WMA, every time an expert makes a wrong prediction, we will decrement their weight. Mirroring the MWUM, we will then use the weights to make a probability distribution over the actions and draw our action from this distribution (instead of deterministically picking the majority vote as the WMA does). == Randomized weighted majority algorithm (RWMA) == The randomized weighted majority algorithm is an attempt to improve the dependence of the mistake bound of the WMA on m {\displaystyle m} . Instead of predicting based on majority vote, the weights, are used as probabilities for choosing the experts in each round and are updated over time (hence the name randomized weighted majority). Precisely, if w i {\displaystyle w_{i}} is the weight of expert i {\displaystyle i} , let W = ∑ i w i {\displaystyle W=\sum _{i}w_{i}} . We will follow expert i {\displaystyle i} with probability w i W {\displaystyle {\frac {w_{i}}{W}}} . This results in the following algorithm: initialize all experts to weight 1. for each round: add all experts' weights together to obtain the total weight W {\displaystyle W} choose expert i {\displaystyle i} randomly with probability w i W {\displaystyle {\frac {w_{i}}{W}}} predict as the chosen expert predicts multiply the weights of all experts who predicted wrongly by β {\displaystyle \beta } The goal is to bound the worst-case expected number of mistakes, assuming that the adversary has to select one of the answers as correct before we make our coin toss. This is a reasonable assumption in, for instance, the stock market example provided above: the variance of a stock price should not depend on the opinions of experts that influence private buy or sell decisions, so we can treat the price change as if it was decided before the experts gave their recommendations for the day. The randomized algorithm is better in the worst case than the deterministic algorithm (weighted majority algorithm): in the latter, the worst case was when the weights were split 50/50. But in the randomized version, since the weights are used as probabilities, there would still be a 50/50 chance of getting it right. In addition, generalizing to multiplying the weights of the incorrect experts by β < 1 {\displaystyle \beta <1} instead of strictly 1 2 {\displaystyle {\frac {1}{2}}} allows us to trade off between dependence on m {\displaystyle m} and log 2 n {\displaystyle \log _{2}n} . This trade-off will be quantified in the analysis section. == Analysis == Let W t {\displaystyle W_{t}} denote the total weight of all experts at round t {\displaystyle t} . Also let F t {\displaystyle F_{t}} denote the fraction of weight placed on experts which predict the wrong answer at round t {\displaystyle t} . Finally, let N {\displaystyle N} be the total number of rounds in the process. By definition, F t {\displaystyle F_{t}} is the probability that the algorithm makes a mistake on round t {\displaystyle t} . It follows from the linearity of expectation that if M {\displaystyle M} denotes the total number of mistakes made during the entire process, E [ M ] = ∑ t = 1 N F t {\displaystyle E[M]=\sum _{t=1}^{N}F_{t}} . After round t {\displaystyle t} , the total weight is decreased by ( 1 − β ) F t W t {\displaystyle \ (1-\beta )F_{t}W_{t}} , since all weights corresponding to a wrong answer are multiplied by β < 1 {\displaystyle \ \beta <1} . It then follows that W t + 1 = W t ( 1 − ( 1 − β ) F t ) {\displaystyle W_{t+1}=W_{t}(1-(1-\beta )F_{t})} . By telescoping, since W 1 = n {\displaystyle W_{1}=n} , it follows that the total weight after the process concludes is On the other hand, suppose that m {\displaystyle \ m} is the number of mistakes made by the best-performing expert. At the end, this expert has weight β m {\displaystyle \ \beta ^{m}} . It follows, then, that the total weight is at least this much; in other words, W ≥ β m {\displaystyle \ W\geq \beta ^{m}} . This inequality and the above result imply Taking the natural logarithm of both sides yields Now, the Taylor series of the natural logarithm is In particular, it follows that ln ( 1 − ( 1 − β ) F t ) < − ( 1 − β ) F t {\displaystyle \ \ln(1-(1-\beta )F_{t})<-(1-\beta )F_{t}} . Thus, Recalling that E [ M ] = ∑ t = 1 N F t {\displaystyle E[M]=\sum _{t=1}^{N}F_{t}} and rearranging, it follows that Now, as β → 1 {\displaystyle \beta \to 1} from below, the first constant tends to 1 {\displaystyle 1} ; however, the second constant tends to + ∞ {\displaystyle +\infty } . To quantify this tradeoff, define ε = 1 − β {\displaystyle \varepsilon =1-\beta } to be the penalty associated with getting a prediction wrong. Then, again applying the Taylor series of the natural logarithm, It then follows that the mistake bound, for small ε {\displaystyle \varepsilon } , can be written in the form ( 1 + ϵ 2 + O ( ε 2 ) ) m + ϵ − 1 ln ( n ) {\displaystyle \ \left(1+{\frac {\epsilon }{2}}+O(\varepsilon ^{2})\right)m+\epsilon ^{-1}\ln(n)} . In English, the less that we penalize experts for their mistakes, the more that additional experts will lead to initial mistakes but the closer we get to capturing the predictive accuracy of the best expert as time goes on. In particular, given a sufficiently low value of ε {\displaystyle \varepsilon } and enough rounds, the randomized weighted majority algorithm can get arbitrarily close to the correct prediction rate of the best expert. In particular, as long as m {\displaystyle m} is sufficiently large compared to ln ( n ) {\displaystyle \ln(n)} (so that their ratio is sufficiently small), we can assign we can obtain an upper bound on the number of mistakes equal to This implies that the "regret bound" on the algorithm (that is, how much worse it performs than the best expert) is sublinear, at O ( m ln ( n ) ) {\displaystyle O({\sqrt {m\ln(n)}})} . == Revisiting the motivation == Recall that the motivation for the randomized weighted majority algorithm was given by an example where the best expert makes a mistake 20% of the time. Precisely, in N = 100 {\displaystyle N=100} rounds, with n = 10 {\displaystyle n=10} experts, where the best expert makes m = 20 {\displaystyle m=20} mistakes, the deterministic weighted majority algorithm only guarantees an upper bound of 2.4 ( log 2 10 + 20 ) ≈ 56 {\displaystyle 2.4(\log _{2}10+20)\approx 56} . By the analysis above, it follows that minimizing the number of worst-case expected mistakes is equivalent to minimizing the fun
Probabilistic latent semantic analysis
Probabilistic latent semantic analysis (PLSA), also known as probabilistic latent semantic indexing (PLSI, especially in information retrieval circles) is a statistical technique for the analysis of two-mode and co-occurrence data. In effect, one can derive a low-dimensional representation of the observed variables in terms of their affinity to certain hidden variables, just as in latent semantic analysis, from which PLSA evolved. Compared to standard latent semantic analysis which stems from linear algebra and downsizes the occurrence tables (usually via a singular value decomposition), probabilistic latent semantic analysis is based on a mixture decomposition derived from a latent class model. == Model == Considering observations in the form of co-occurrences ( w , d ) {\displaystyle (w,d)} of words and documents, PLSA models the probability of each co-occurrence as a mixture of conditionally independent multinomial distributions: P ( w , d ) = ∑ c P ( d ) P ( c | d ) P ( w | c ) = P ( d ) ∑ c P ( c | d ) P ( w | c ) {\displaystyle P(w,d)=\sum _{c}P(d)P(c|d)P(w|c)=P(d)\sum _{c}P(c|d)P(w|c)} with c {\displaystyle c} being the words' topic. Note that the number of topics is a hyperparameter that must be chosen in advance and is not estimated from the data. The first formulation is the symmetric formulation, where w {\displaystyle w} and d {\displaystyle d} are both generated from the latent class c {\displaystyle c} in similar ways (using the conditional probabilities P ( d | c ) {\displaystyle P(d|c)} and P ( w | c ) {\displaystyle P(w|c)} ), whereas the second formulation is the asymmetric formulation, where, for each document d {\displaystyle d} , a latent class is chosen conditionally to the document according to P ( c | d ) {\displaystyle P(c|d)} , and a word is then generated from that class according to P ( w | c ) {\displaystyle P(w|c)} . Although we have used words and documents in this example, the co-occurrence of any couple of discrete variables may be modelled in exactly the same way. So, the number of parameters is equal to c d + w c {\displaystyle cd+wc} . The number of parameters grows linearly with the number of documents. In addition, although PLSA is a generative model of the documents in the collection it is estimated on, it is not a generative model of new documents. Their parameters are learned using the EM algorithm. == Application == PLSA may be used in a discriminative setting, via Fisher kernels. PLSA has applications in information retrieval and filtering, natural language processing, machine learning from text, bioinformatics, and related areas. It is reported that the aspect model used in the probabilistic latent semantic analysis has severe overfitting problems. == Extensions == Hierarchical extensions: Asymmetric: MASHA ("Multinomial ASymmetric Hierarchical Analysis") Symmetric: HPLSA ("Hierarchical Probabilistic Latent Semantic Analysis") Generative models: The following models have been developed to address an often-criticized shortcoming of PLSA, namely that it is not a proper generative model for new documents. Latent Dirichlet allocation – adds a Dirichlet prior on the per-document topic distribution Higher-order data: Although this is rarely discussed in the scientific literature, PLSA extends naturally to higher order data (three modes and higher), i.e. it can model co-occurrences over three or more variables. In the symmetric formulation above, this is done simply by adding conditional probability distributions for these additional variables. This is the probabilistic analogue to non-negative tensor factorisation. == History == This is an example of a latent class model (see references therein), and it is related to non-negative matrix factorization. The present terminology was coined in 1999 by Thomas Hofmann.
Secure state
A secure state is an information systems security term to describe where entities in a computer system are divided into subjects and objects, and it can be formally proven that each state transition preserves security by moving from one secure state to another secure state. Thereby it can be inductively proven that the system is secure. As defined in the Bell–LaPadula model, the secure state is built on the concept of a state machine with a set of allowable states in a system. The transition from one state to another state is defined by transition functions. A system state is defined to be "secure" if the only permitted access modes of subjects to objects are in accordance with a security policy.
Blockmodeling linked networks
Blockmodeling linked networks is an approach in blockmodeling in analysing the linked networks. Such approach is based on the generalized multilevel blockmodeling approach. The main objective of this approach is to achieve clustering of the nodes from all involved sets, while at the same time using all available information. At the same time, all one-mode and two-node networks, that are connected, are blockmodeled, which results in obtaining only one clustering, using nodes from each sets. Each cluster ideally contains only nodes from one set, which also allows the modeling of the links among clusters from different sets (through two-mode networks). This approach was introduced by Aleš Žiberna in 2014. Blockmodeling linked networks can be done using: separate analysis: blockmodeling each level separately; conversion approach: converting all one-mode networks to the same level and joining with two-mode networks; a true multilevel approach: one-mode and two-mode networks are blockmodeled at the same time, resulting in one clustering for nodes from each level.