AI Chat Bots Like Character AI

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  • Netomi

    Netomi

    Netomi, formerly msg.ai, is an American artificial intelligence company and developer of chatbot technologies. == History == msg.ai was founded in May 2015 by Puneet Mehta. msg.ai worked with Sony Pictures to launch a chat bot on Facebook Messenger for a $100M film, Goosebumps and subsequently joined Y Combinator as a member of the Winter 2016 class. Later that year and in 2017, msg.ai completed two rounds of seed funding, led by Y Combinator and Index Ventures. In 2018, the company changed its name to Netomi. In 2019, the company raised $14.7 million in a Series A funding round also led by Index Ventures. In 2021, the company raised $30 million in a Series B funding round led by WndrCo LLC.

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  • Aleph (ILP)

    Aleph (ILP)

    Aleph (A Learning Engine for Proposing Hypotheses) is an inductive logic programming system introduced by Ashwin Srinivasan in 2001. As of 2022 it is still one of the most widely used inductive logic programming systems. It is based on the earlier system Progol. == Learning task == The input to Aleph is background knowledge, specified as a logic program, a language bias in the form of mode declarations, as well as positive and negative examples specified as ground facts. As output it returns a logic program which, together with the background knowledge, entails all of the positive examples and none of the negative examples. == Basic algorithm == Starting with an empty hypothesis, Aleph proceeds as follows: It chooses a positive example to generalise; if none are left, it aborts and outputs the current hypothesis. Then it constructs the bottom clause, that is, the most specific clause that is allowed by the mode declarations and covers the example. It then searches for a generalisation of the bottom clause that scores better on the chosen metric. It then adds the new clause to the hypothesis program and removes all examples that are covered by the new clause. == Search algorithm == Aleph searches for clauses in a top-down manner, using the bottom clause constructed in the preceding step to bound the search from below. It searches the refinement graph in a breadth-first manner, with tunable parameters to bound the maximal clause size and proof depth. It scores each clause using one of 13 different evaluation metrics, as chosen in advance by the user.

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  • Alternating decision tree

    Alternating decision tree

    An alternating decision tree (ADTree) is a machine learning method for classification. It generalizes decision trees and has connections to boosting. An ADTree consists of an alternation of decision nodes, which specify a predicate condition, and prediction nodes, which contain a single number. An instance is classified by an ADTree by following all paths for which all decision nodes are true, and summing any prediction nodes that are traversed. == History == ADTrees were introduced by Yoav Freund and Llew Mason. However, the algorithm as presented had several typographical errors. Clarifications and optimizations were later presented by Bernhard Pfahringer, Geoffrey Holmes and Richard Kirkby. Implementations are available in Weka and JBoost. == Motivation == Original boosting algorithms typically used either decision stumps or decision trees as weak hypotheses. As an example, boosting decision stumps creates a set of T {\displaystyle T} weighted decision stumps (where T {\displaystyle T} is the number of boosting iterations), which then vote on the final classification according to their weights. Individual decision stumps are weighted according to their ability to classify the data. Boosting a simple learner results in an unstructured set of T {\displaystyle T} hypotheses, making it difficult to infer correlations between attributes. Alternating decision trees introduce structure to the set of hypotheses by requiring that they build off a hypothesis that was produced in an earlier iteration. The resulting set of hypotheses can be visualized in a tree based on the relationship between a hypothesis and its "parent." Another important feature of boosted algorithms is that the data is given a different distribution at each iteration. Instances that are misclassified are given a larger weight while accurately classified instances are given reduced weight. == Alternating decision tree structure == An alternating decision tree consists of decision nodes and prediction nodes. Decision nodes specify a predicate condition. Prediction nodes contain a single number. ADTrees always have prediction nodes as both root and leaves. An instance is classified by an ADTree by following all paths for which all decision nodes are true and summing any prediction nodes that are traversed. This is different from binary classification trees such as CART (Classification and regression tree) or C4.5 in which an instance follows only one path through the tree. === Example === The following tree was constructed using JBoost on the spambase dataset (available from the UCI Machine Learning Repository). In this example, spam is coded as 1 and regular email is coded as −1. The following table contains part of the information for a single instance. The instance is scored by summing all of the prediction nodes through which it passes. In the case of the instance above, the score is calculated as The final score of 0.657 is positive, so the instance is classified as spam. The magnitude of the value is a measure of confidence in the prediction. The original authors list three potential levels of interpretation for the set of attributes identified by an ADTree: Individual nodes can be evaluated for their own predictive ability. Sets of nodes on the same path may be interpreted as having a joint effect The tree can be interpreted as a whole. Care must be taken when interpreting individual nodes as the scores reflect a re weighting of the data in each iteration. == Description of the algorithm == The inputs to the alternating decision tree algorithm are: A set of inputs ( x 1 , y 1 ) , … , ( x m , y m ) {\displaystyle (x_{1},y_{1}),\ldots ,(x_{m},y_{m})} where x i {\displaystyle x_{i}} is a vector of attributes and y i {\displaystyle y_{i}} is either -1 or 1. Inputs are also called instances. A set of weights w i {\displaystyle w_{i}} corresponding to each instance. The fundamental element of the ADTree algorithm is the rule. A single rule consists of a precondition, a condition, and two scores. A condition is a predicate of the form "attribute value." A precondition is simply a logical conjunction of conditions. Evaluation of a rule involves a pair of nested if statements: 1 if (precondition) 2 if (condition) 3 return score_one 4 else 5 return score_two 6 end if 7 else 8 return 0 9 end if Several auxiliary functions are also required by the algorithm: W + ( c ) {\displaystyle W_{+}(c)} returns the sum of the weights of all positively labeled examples that satisfy predicate c {\displaystyle c} W − ( c ) {\displaystyle W_{-}(c)} returns the sum of the weights of all negatively labeled examples that satisfy predicate c {\displaystyle c} W ( c ) = W + ( c ) + W − ( c ) {\displaystyle W(c)=W_{+}(c)+W_{-}(c)} returns the sum of the weights of all examples that satisfy predicate c {\displaystyle c} The algorithm is as follows: 1 function ad_tree 2 input Set of m training instances 3 4 wi = 1/m for all i 5 a = 1 2 ln W + ( t r u e ) W − ( t r u e ) {\displaystyle a={\frac {1}{2}}{\textrm {ln}}{\frac {W_{+}(true)}{W_{-}(true)}}} 6 R0 = a rule with scores a and 0, precondition "true" and condition "true." 7 P = { t r u e } {\displaystyle {\mathcal {P}}=\{true\}} 8 C = {\displaystyle {\mathcal {C}}=} the set of all possible conditions 9 for j = 1 … T {\displaystyle j=1\dots T} 10 p ∈ P , c ∈ C {\displaystyle p\in {\mathcal {P}},c\in {\mathcal {C}}} get values that minimize z = 2 ( W + ( p ∧ c ) W − ( p ∧ c ) + W + ( p ∧ ¬ c ) W − ( p ∧ ¬ c ) ) + W ( ¬ p ) {\displaystyle z=2\left({\sqrt {W_{+}(p\wedge c)W_{-}(p\wedge c)}}+{\sqrt {W_{+}(p\wedge \neg c)W_{-}(p\wedge \neg c)}}\right)+W(\neg p)} 11 P + = p ∧ c + p ∧ ¬ c {\displaystyle {\mathcal {P}}+=p\wedge c+p\wedge \neg c} 12 a 1 = 1 2 ln W + ( p ∧ c ) + 1 W − ( p ∧ c ) + 1 {\displaystyle a_{1}={\frac {1}{2}}{\textrm {ln}}{\frac {W_{+}(p\wedge c)+1}{W_{-}(p\wedge c)+1}}} 13 a 2 = 1 2 ln W + ( p ∧ ¬ c ) + 1 W − ( p ∧ ¬ c ) + 1 {\displaystyle a_{2}={\frac {1}{2}}{\textrm {ln}}{\frac {W_{+}(p\wedge \neg c)+1}{W_{-}(p\wedge \neg c)+1}}} 14 Rj = new rule with precondition p, condition c, and weights a1 and a2 15 w i = w i e − y i R j ( x i ) {\displaystyle w_{i}=w_{i}e^{-y_{i}R_{j}(x_{i})}} 16 end for 17 return set of Rj The set P {\displaystyle {\mathcal {P}}} grows by two preconditions in each iteration, and it is possible to derive the tree structure of a set of rules by making note of the precondition that is used in each successive rule. == Empirical results == Figure 6 in the original paper demonstrates that ADTrees are typically as robust as boosted decision trees and boosted decision stumps. Typically, equivalent accuracy can be achieved with a much simpler tree structure than recursive partitioning algorithms.

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  • Clustering illusion

    Clustering illusion

    The clustering illusion is the tendency to erroneously consider the inevitable "streaks" or "clusters" arising in small samples from random distributions to be non-random. The illusion is caused by a human tendency to underpredict the amount of variability likely to appear in a small sample of random or pseudorandom data. Thomas Gilovich, an early author on the subject, argued that the effect occurs for different types of random dispersions. Some might perceive patterns in stock market price fluctuations over time, or clusters in two-dimensional data such as the locations of impact of World War II V-1 flying bombs on maps of London. Although Londoners developed specific theories about the pattern of impacts within London, a statistical analysis by R. D. Clarke originally published in 1946 showed that the impacts of V-2 rockets on London were a close fit to a random distribution. == Similar biases == Using this cognitive bias in causal reasoning may result in the Texas sharpshooter fallacy, in which differences in data are ignored and similarities are overemphasized. More general forms of erroneous pattern recognition are pareidolia and apophenia. Related biases are the illusion of control which the clustering illusion could contribute to, and insensitivity to sample size in which people don't expect greater variation in smaller samples. A different cognitive bias involving misunderstanding of chance streams is the gambler's fallacy. == Possible causes == Daniel Kahneman and Amos Tversky explained this kind of misprediction as being caused by the representativeness heuristic (which itself they also first proposed).

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  • Symbol level

    Symbol level

    In knowledge-based systems, agents choose actions based on the principle of rationality to move closer to a desired goal. The agent is able to make decisions based on knowledge it has about the world (see knowledge level). But for the agent to actually change its state, it must use whatever means it has available. This level of description for the agent's behavior is the symbol level. The term was coined by Allen Newell in 1982. For example, in a computer program, the knowledge level consists of the information contained in its data structures that it uses to perform certain actions. The symbol level consists of the program's algorithms, the data structures themselves, and so on.

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  • Evolutionary attractor

    Evolutionary attractor

    An evolutionary attractor is a point in an evolutionary space where a selection process will always drive trait values towards that point from the region around it. Because of the importance of evolution through natural selection, often such an evolutionary space will be defined by genetic or phenotypic traits, or possibly both. In this case the selection process will be a form of natural selection. The existence of an evolutionary attractor in a biological evolutionary space does not always imply that it can be reached from all points in that evolutionary space, nor does it identify what will happen when the evolutionary attractor is reached. While an evolutionary attractor may represent a point in evolutionary space that is resistant to further selection, such as an evolutionarily stable strategy, other possibilities are available. Because identification of an evolutionary attractor on its own does not describe everything about the evolutionary space in which it lies, this has led to interest in the evolutionary dynamics surrounding evolutionary attractors and in evolutionary spaces in general. (Theoretical biologists and mathematicians working in the area may prefer the terms adaptive dynamics or evolutionary invasion analysis to evolutionary dynamics.) These fields use differential equations which allows a more complete understanding of the dynamics in evolutionary spaces including the existence or otherwise of evolutionary attractors. Advances in the study of molecular evolution have also led to the identification of evolutionary attractors at a molecular level. Because biological evolutionary processes have been studied using evolutionary game theory, a technique inspired by game theory originally derived to address economic problems, not only can evolutionary attractors be found in biology but economists studying evolutionary economic models have also identified evolutionary attractors. Evolution in biology has also inspired evolutionary computation in computer science. Many algorithms in this field use a form of selection inspired by natural selection to generate results through evolutionary algorithms. This is therefore another area in which evolutionary attractors have been identified. == Evolutionary attractors in biology == It is not probably not surprising that biology is the field where most examples of evolutionary attractors have been identified, given the importance of evolution through natural selection. === Evolutionary attractors in adaptive landscapes === An evolutionary attractor is a point in genetic and/or phenotypic trait space, that evolution will always drive trait values towards via a selection process. The concept of an evolutionary attractor arose in population genetics following the origin of the adaptive landscape originally proposed by Sewall Wright in 1932. The height of a point in an adaptive landscape is a measure of evolutionary fitness. If a point in an adaptive landscape is a peak, then selection will always drive traits towards it and it will be an evolutionary attractor. While population genetics deals with discrete genetic traits, quantitative genetics extended such concepts to deal with continuous genetic traits, where the concept of evolutionary attractor is also valid. === Evolutionary attractors in evolutionary game models === Evolutionary game theory introduced into evolutionary biology concepts originally used in economics, with the advantage that evolution could be studied in relation to strategic choices made in animal conflicts. This is of particular interest because of the concept of the evolutionarily stable strategy or ESS, a strategy that once established is resistant to invasion by other strategies. ESSs will not always be evolutionary attractors, but if they are they will persist over evolutionary time. === Dynamics around evolutionary attractors in biology === Evolutionary attractors in biology do not exist in isolation. By definition they must exist in an evolutionary trait space where selection drives all traits towards them from a region immediately around them. That is, they must be convergence stable. Eshel (1983) modified the definition of an ESS by considering individually advantageous reduction from a majority deviation: he created the term continuous stability. A continuously stable ESS can be shown to be convergence stable, therefore it will act as an evolutionary attractor. But the nature of evolutionary trait spaces in biology means that it is not possible to guarantee that the region of convergence to the evolutionary attractor covers the whole of the trait space, nor that there is only one evolutionary attractor in a particular trait space. These issues have led to the emergence of the related fields of evolutionary dynamics, adaptive dynamics and evolutionary invasion analysis, all of which use differential equations to understand the dynamics in evolutionary trait spaces. Hence, if one or more evolutionary attractor exists in an evolutionary trait space, they provide techniques to understand the dynamics in that trait space around the evolutionary attractor. === Evolutionary attractors in an ecological context === Evolution in biology does not take place in single species in isolation. Ecological interaction of species leads to coevolution. Important examples of this are host-parasite or host-pathogen interaction, which can make both the dynamics around evolutionary attractors more complex, and the occurrence and number of evolutionary attractors more diverse. Evolutionary attractors have been identified in the analysis of evolutionary epidemiology of plant pathogens. In the above study working on plant populations the authors were able to identify evolutionary attractors using methods from adaptive dynamics. A model applied to the analysis of a maize (Zea mays L.) virus identified convergence stable equilibria through simulation modelling. A related model identified evolutionary attractors in the interaction of plants with fungal pathogens. === Evolutionary attractors in molecular genetics === As mentioned above much of the consideration of evolutionary attractors in biology has been through investigation of selection at a genetic or phenotypic level or both, in a single species or in coevolving species. Advances in the study of molecular genetics now allow the study of evolutionary attractors to be taken to a molecular genetic level. Wilson et. al (2019) studied the evolution of gene regulatory networks and identified the emergence of evolutionary attractors. == Evolutionary attractors in economics == Evolutionary game theory as applied in biology was inspired by game theory originally devised for applications in economics. Game theory remains an active field of research outside of biology, and thus it is not surprising that researchers in evolutionary economics use evolutionary game theory. Evolutionary attractors have been demonstrated by economists studying the evolutionary dynamics of market entry with market dynamics based on the replicator dynamics of biological evolutionary games. == Evolutionary attractors in computing == Evolutionary computation is a branch of computer science inspired by biological evolution. Many algorithms in evolutionary computation use a form of selection. Thus evolutionary attractors have been identified in computer science as well as in biology and economics. Evolutionary algorithms have generated evolutionary attractors, probably because of the similarity between adaptive hill-climbing in evolutionary heuristics and the adaptive landscape originated to explain evolution through natural selection.

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  • Diffusion model

    Diffusion model

    In machine learning, diffusion models, also known as diffusion-based generative models or score-based generative models, are a class of latent variable generative models. A diffusion model consists of two major components: the forward diffusion process, and the reverse sampling process. The goal of diffusion models is to learn a diffusion process for a given dataset, such that the process can generate new elements that are distributed similarly as the original dataset. A diffusion model models data as generated by a diffusion process, whereby a new datum performs a random walk with drift through the space of all possible data. A trained diffusion model can be sampled in many ways, with different efficiency and quality. There are various equivalent formalisms, including Markov chains, denoising diffusion probabilistic models, noise conditioned score networks, and stochastic differential equations. They are typically trained using variational inference. The model responsible for denoising is typically called its "backbone". The backbone may be of any kind, but they are typically U-nets or transformers. As of 2024, diffusion models are mainly used for computer vision tasks, including image denoising, inpainting, super-resolution, image generation, and video generation. These typically involve training a neural network to sequentially denoise images blurred with Gaussian noise. The model is trained to reverse the process of adding noise to an image. After training to convergence, it can be used for image generation by starting with an image composed of random noise, and applying the network iteratively to denoise the image. Diffusion-based image generators have seen widespread commercial interest, such as Stable Diffusion and DALL-E. These models typically combine diffusion models with other models, such as text-encoders and cross-attention modules to allow text-conditioned generation. Other than computer vision, diffusion models have also found applications in natural language processing such as text generation and summarization, sound generation, and reinforcement learning. == Denoising diffusion model == === Non-equilibrium thermodynamics === Diffusion models were introduced in 2015 as a method to train a model that can sample from a highly complex probability distribution. They used techniques from non-equilibrium thermodynamics, especially diffusion. Consider, for example, how one might model the distribution of all naturally occurring photos. Each image is a point in the space of all images, and the distribution of naturally occurring photos is a "cloud" in space, which, by repeatedly adding noise to the images, diffuses out to the rest of the image space, until the cloud becomes all but indistinguishable from a Gaussian distribution N ( 0 , I ) {\displaystyle {\mathcal {N}}(0,I)} . A model that can approximately undo the diffusion can then be used to sample from the original distribution. This is studied in "non-equilibrium" thermodynamics, as the starting distribution is not in equilibrium, unlike the final distribution. The equilibrium distribution is the Gaussian distribution N ( 0 , I ) {\displaystyle {\mathcal {N}}(0,I)} , with pdf ρ ( x ) ∝ e − 1 2 ‖ x ‖ 2 {\displaystyle \rho (x)\propto e^{-{\frac {1}{2}}\|x\|^{2}}} . This is just the Maxwell–Boltzmann distribution of particles in a potential well V ( x ) = 1 2 ‖ x ‖ 2 {\displaystyle V(x)={\frac {1}{2}}\|x\|^{2}} at temperature 1. The initial distribution, being very much out of equilibrium, would diffuse towards the equilibrium distribution, making biased random steps that are a sum of pure randomness (like a Brownian walker) and gradient descent down the potential well. The randomness is necessary: if the particles were to undergo only gradient descent, then they will all fall to the origin, collapsing the distribution. === Denoising Diffusion Probabilistic Model (DDPM) === The 2020 paper proposed the Denoising Diffusion Probabilistic Model (DDPM), which improves upon the previous method by variational inference. ==== Forward diffusion ==== To present the model, some notation is required. β 1 , . . . , β T ∈ ( 0 , 1 ) {\displaystyle \beta _{1},...,\beta _{T}\in (0,1)} are fixed constants. α t := 1 − β t {\displaystyle \alpha _{t}:=1-\beta _{t}} α ¯ t := α 1 ⋯ α t {\displaystyle {\bar {\alpha }}_{t}:=\alpha _{1}\cdots \alpha _{t}} σ t := 1 − α ¯ t {\displaystyle \sigma _{t}:={\sqrt {1-{\bar {\alpha }}_{t}}}} σ ~ t := σ t − 1 σ t β t {\displaystyle {\tilde {\sigma }}_{t}:={\frac {\sigma _{t-1}}{\sigma _{t}}}{\sqrt {\beta _{t}}}} μ ~ t ( x t , x 0 ) := α t ( 1 − α ¯ t − 1 ) x t + α ¯ t − 1 ( 1 − α t ) x 0 σ t 2 {\displaystyle {\tilde {\mu }}_{t}(x_{t},x_{0}):={\frac {{\sqrt {\alpha _{t}}}(1-{\bar {\alpha }}_{t-1})x_{t}+{\sqrt {{\bar {\alpha }}_{t-1}}}(1-\alpha _{t})x_{0}}{\sigma _{t}^{2}}}} N ( μ , Σ ) {\displaystyle {\mathcal {N}}(\mu ,\Sigma )} is the normal distribution with mean μ {\displaystyle \mu } and variance Σ {\displaystyle \Sigma } , and N ( x | μ , Σ ) {\displaystyle {\mathcal {N}}(x|\mu ,\Sigma )} is the probability density at x {\displaystyle x} . A vertical bar denotes conditioning. A forward diffusion process starts at some starting point x 0 ∼ q {\displaystyle x_{0}\sim q} , where q {\displaystyle q} is the probability distribution to be learned, then repeatedly adds noise to it by x t = 1 − β t x t − 1 + β t z t {\displaystyle x_{t}={\sqrt {1-\beta _{t}}}x_{t-1}+{\sqrt {\beta _{t}}}z_{t}} where z 1 , . . . , z T {\displaystyle z_{1},...,z_{T}} are IID (Independent and identically distributed random variables) samples from N ( 0 , I ) {\displaystyle {\mathcal {N}}(0,I)} . The coefficients 1 − β t {\displaystyle {\sqrt {1-\beta _{t}}}} and β t {\displaystyle {\sqrt {\beta _{t}}}} ensure that Var ( X t ) = I {\displaystyle {\mbox{Var}}(X_{t})=I} assuming that Var ( X 0 ) = I {\displaystyle {\mbox{Var}}(X_{0})=I} . The values of β t {\displaystyle \beta _{t}} are chosen such that for any starting distribution of x 0 {\displaystyle x_{0}} , if it has finite second moment, then lim t → ∞ x t | x 0 {\displaystyle \lim _{t\to \infty }x_{t}|x_{0}} converges to N ( 0 , I ) {\displaystyle {\mathcal {N}}(0,I)} . The entire diffusion process then satisfies q ( x 0 : T ) = q ( x 0 ) q ( x 1 | x 0 ) ⋯ q ( x T | x T − 1 ) = q ( x 0 ) N ( x 1 | α 1 x 0 , β 1 I ) ⋯ N ( x T | α T x T − 1 , β T I ) {\displaystyle q(x_{0:T})=q(x_{0})q(x_{1}|x_{0})\cdots q(x_{T}|x_{T-1})=q(x_{0}){\mathcal {N}}(x_{1}|{\sqrt {\alpha _{1}}}x_{0},\beta _{1}I)\cdots {\mathcal {N}}(x_{T}|{\sqrt {\alpha _{T}}}x_{T-1},\beta _{T}I)} or ln ⁡ q ( x 0 : T ) = ln ⁡ q ( x 0 ) − ∑ t = 1 T 1 2 β t ‖ x t − 1 − β t x t − 1 ‖ 2 + C {\displaystyle \ln q(x_{0:T})=\ln q(x_{0})-\sum _{t=1}^{T}{\frac {1}{2\beta _{t}}}\|x_{t}-{\sqrt {1-\beta _{t}}}x_{t-1}\|^{2}+C} where C {\displaystyle C} is a normalization constant and often omitted. In particular, we note that x 1 : T | x 0 {\displaystyle x_{1:T}|x_{0}} is a Gaussian process, which affords us considerable freedom in reparameterization. For example, by standard manipulation with Gaussian process, x t | x 0 ∼ N ( α ¯ t x 0 , σ t 2 I ) {\displaystyle x_{t}|x_{0}\sim N\left({\sqrt {{\bar {\alpha }}_{t}}}x_{0},\sigma _{t}^{2}I\right)} x t − 1 | x t , x 0 ∼ N ( μ ~ t ( x t , x 0 ) , σ ~ t 2 I ) {\displaystyle x_{t-1}|x_{t},x_{0}\sim {\mathcal {N}}({\tilde {\mu }}_{t}(x_{t},x_{0}),{\tilde {\sigma }}_{t}^{2}I)} In particular, notice that for large t {\displaystyle t} , the variable x t | x 0 ∼ N ( α ¯ t x 0 , σ t 2 I ) {\displaystyle x_{t}|x_{0}\sim N\left({\sqrt {{\bar {\alpha }}_{t}}}x_{0},\sigma _{t}^{2}I\right)} converges to N ( 0 , I ) {\displaystyle {\mathcal {N}}(0,I)} . That is, after a long enough diffusion process, we end up with some x T {\displaystyle x_{T}} that is very close to N ( 0 , I ) {\displaystyle {\mathcal {N}}(0,I)} , with all traces of the original x 0 ∼ q {\displaystyle x_{0}\sim q} gone. For example, since x t | x 0 ∼ N ( α ¯ t x 0 , σ t 2 I ) {\displaystyle x_{t}|x_{0}\sim N\left({\sqrt {{\bar {\alpha }}_{t}}}x_{0},\sigma _{t}^{2}I\right)} we can sample x t | x 0 {\displaystyle x_{t}|x_{0}} directly "in one step", instead of going through all the intermediate steps x 1 , x 2 , . . . , x t − 1 {\displaystyle x_{1},x_{2},...,x_{t-1}} . ==== Backward diffusion ==== The key idea of DDPM is to use a neural network parametrized by θ {\displaystyle \theta } . The network takes in two arguments x t , t {\displaystyle x_{t},t} , and outputs a vector μ θ ( x t , t ) {\displaystyle \mu _{\theta }(x_{t},t)} and a matrix Σ θ ( x t , t ) {\displaystyle \Sigma _{\theta }(x_{t},t)} , such that each step in the forward diffusion process can be approximately undone by x t − 1 ∼ N ( μ θ ( x t , t ) , Σ θ ( x t , t ) ) {\displaystyle x_{t-1}\sim {\mathcal {N}}(\mu _{\theta }(x_{t},t),\Sigma _{\theta }(x_{t},t))} . This then gives us a backward diffusion process p θ {\displaystyle p_{\theta }} defined by p θ ( x T ) = N ( x T | 0 , I ) {\displaystyle p_{\theta }(x

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  • Random forest

    Random forest

    Random forests or random decision forests is an ensemble learning method for classification, regression and other tasks that works by creating a multitude of decision trees during training. For classification tasks, the output of the random forest is the class selected by most trees. For regression tasks, the output is the average of the predictions of the trees. Random forests correct for decision trees' habit of overfitting to their training set. The first algorithm for random decision forests was created in 1995 by Tin Kam Ho using the random subspace method, which, in Ho's formulation, is a way to implement the "stochastic discrimination" approach to classification proposed by Eugene Kleinberg. An extension of the algorithm was developed by Leo Breiman and Adele Cutler, who registered "Random Forests" as a trademark in 2006 (as of 2019, owned by Minitab, Inc.). The extension combines Breiman's "bagging" idea and random selection of features, introduced first by Ho and later independently by Amit and Geman in order to construct a collection of decision trees with controlled variance. == History == The general method of random decision forests was first proposed by Salzberg and Heath in 1993, with a method that used a randomized decision tree algorithm to create multiple trees and then combine them using majority voting. This idea was developed further by Ho in 1995. Ho established that forests of trees splitting with oblique hyperplanes can gain accuracy as they grow without suffering from overtraining, as long as the forests are randomly restricted to be sensitive to only selected feature dimensions. A subsequent work along the same lines concluded that other splitting methods behave similarly, as long as they are randomly forced to be insensitive to some feature dimensions. This observation that a more complex classifier (a larger forest) gets more accurate nearly monotonically is in sharp contrast to the common belief that the complexity of a classifier can only grow to a certain level of accuracy before being hurt by overfitting. The explanation of the forest method's resistance to overtraining can be found in Kleinberg's theory of stochastic discrimination. The early development of Breiman's notion of random forests was influenced by the work of Amit and Geman who introduced the idea of searching over a random subset of the available decisions when splitting a node, in the context of growing a single tree. The idea of random subspace selection from Ho was also influential in the design of random forests. This method grows a forest of trees, and introduces variation among the trees by projecting the training data into a randomly chosen subspace before fitting each tree or each node. Finally, the idea of randomized node optimization, where the decision at each node is selected by a randomized procedure, rather than a deterministic optimization was first introduced by Thomas G. Dietterich. The proper introduction of random forests was made in a paper by Leo Breiman, that has become one of the world's most cited papers. This paper describes a method of building a forest of uncorrelated trees using a CART like procedure, combined with randomized node optimization and bagging. In addition, this paper combines several ingredients, some previously known and some novel, which form the basis of the modern practice of random forests, in particular: Using out-of-bag error as an estimate of the generalization error. Measuring variable importance through permutation. The report also offers the first theoretical result for random forests in the form of a bound on the generalization error which depends on the strength of the trees in the forest and their correlation. == Algorithm == === Preliminaries: decision tree learning === Decision trees are a popular method for various machine learning tasks. Tree learning is almost "an off-the-shelf procedure for data mining", say Hastie et al., "because it is invariant under scaling and various other transformations of feature values, is robust to inclusion of irrelevant features, and produces inspectable models. However, they are seldom accurate". In particular, trees that are grown very deep tend to learn highly irregular patterns: they overfit their training sets, i.e. have low bias, but very high variance. Random forests are a way of averaging multiple deep decision trees, trained on different parts of the same training set, with the goal of reducing the variance. This comes at the expense of a small increase in the bias and some loss of interpretability, but generally greatly boosts the performance in the final model. === Bagging === The training algorithm for random forests applies the general technique of bootstrap aggregating, or bagging, to tree learners. Given a training set X = x1, ..., xn with responses Y = y1, ..., yn, bagging repeatedly (B times) selects a random sample with replacement of the training set and fits trees to these samples: After training, predictions for unseen samples x' can be made by averaging the predictions from all the individual regression trees on x': f ^ = 1 B ∑ b = 1 B f b ( x ′ ) {\displaystyle {\hat {f}}={\frac {1}{B}}\sum _{b=1}^{B}f_{b}(x')} or by taking the plurality vote in the case of classification trees. This bootstrapping procedure leads to better model performance because it decreases the variance of the model, without increasing the bias. This means that while the predictions of a single tree are highly sensitive to noise in its training set, the average of many trees is not, as long as the trees are not correlated. Simply training many trees on a single training set would give strongly correlated trees (or even the same tree many times, if the training algorithm is deterministic); bootstrap sampling is a way of de-correlating the trees by showing them different training sets. Additionally, an estimate of the uncertainty of the prediction can be made as the standard deviation of the predictions from all the individual regression trees on x′: σ = ∑ b = 1 B ( f b ( x ′ ) − f ^ ) 2 B − 1 . {\displaystyle \sigma ={\sqrt {\frac {\sum _{b=1}^{B}(f_{b}(x')-{\hat {f}})^{2}}{B-1}}}.} The number B of samples (equivalently, of trees) is a free parameter. Typically, a few hundred to several thousand trees are used, depending on the size and nature of the training set. B can be optimized using cross-validation, or by observing the out-of-bag error: the mean prediction error on each training sample xi, using only the trees that did not have xi in their bootstrap sample. The training and test error tend to level off after some number of trees have been fit. === From bagging to random forests === The above procedure describes the original bagging algorithm for trees. Random forests also include another type of bagging scheme: they use a modified tree learning algorithm that selects, at each candidate split in the learning process, a random subset of the features. This process is sometimes called "feature bagging". The reason for doing this is the correlation of the trees in an ordinary bootstrap sample: if one or a few features are very strong predictors for the response variable (target output), these features will be selected in many of the B trees, causing them to become correlated. An analysis of how bagging and random subspace projection contribute to accuracy gains under different conditions is given by Ho. Typically, for a classification problem with p {\displaystyle p} features, p {\displaystyle {\sqrt {p}}} (rounded down) features are used in each split. For regression problems the inventors recommend p / 3 {\displaystyle p/3} (rounded down) with a minimum node size of 5 as the default. In practice, the best values for these parameters should be tuned on a case-to-case basis for every problem. === ExtraTrees === Adding one further step of randomization yields extremely randomized trees, or ExtraTrees. As with ordinary random forests, they are an ensemble of individual trees, but there are two main differences: (1) each tree is trained using the whole learning sample (rather than a bootstrap sample), and (2) the top-down splitting is randomized: for each feature under consideration, a number of random cut-points are selected, instead of computing the locally optimal cut-point (based on, e.g., information gain or the Gini impurity). The values are chosen from a uniform distribution within the feature's empirical range (in the tree's training set). Then, of all the randomly chosen splits, the split that yields the highest score is chosen to split the node. Similar to ordinary random forests, the number of randomly selected features to be considered at each node can be specified. Default values for this parameter are p {\displaystyle {\sqrt {p}}} for classification and p {\displaystyle p} for regression, where p {\displaystyle p} is the number of features in the model. === Random forests for high-dimensional data === The basic random forest procedure may

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  • Play Integrity API

    Play Integrity API

    Play Integrity API (formerly known as SafetyNet) consists of several application programming interfaces (APIs) offered by the Google Play Services to support security sensitive applications and enforce DRM. Currently, these APIs include device integrity verification, app verification, recaptcha and web address verification. It uses an environment called DroidGuard to perform the attestation. == Attestation == The SafetyNet Attestation API, one of the APIs under the SafetyNet umbrella, provides verification that the integrity of the device is not compromised. In practice, non-official ROMs such as LineageOS fail the hardware attestation and thus prevent the user from using a non-compliant ROM with third-party apps (mainly banking) that require the API. Due to this, some consider this a monopolistic practice deterring the entrance of competing mobile operating systems in the market. It requires a network connection to Google servers and validates the hardware signatures. Amongst the checks, the API looks for bootloader unlock status, ROM signatures, kernel strings, it also uses AVB2.0 and dm-verity attestations. Upon successful checks, Google Play will mark the device as Certified. The attestation runs in an environment called DroidGuard (com.google.android.gms.unstable). The SafetyNet Attestation API (one of the four APIs under the SafetyNet umbrella) has been deprecated. As of 6 October 2023, Google planned to replace it with the Play Integrity API by the end of January 2025. The transition ended on 20 May 2025, breaking applications which hadn't been updated. These attestations are offered by Google Play Services and thus are not available on free Android environments, like AOSP. Therefore, developers can require the API to be available and may refuse to execute on AOSP builds. == Google Play Protect == Under the same umbrella, Play Protect is a mechanism to find and remove "vulnerable" apps from one's Android device as well as store apps. Although it's meant to scan for malware-containing apps, it also looks for non-DRM compliant apps. == Criticism == Multiple groups have criticised SafetyNet and the Play Integrity API. Criticisms include that it offers weaker protection compared to alternatives such as Android's hardware attestation API, which provides a stronger form of verification while having the ability to remain compatible with more secure Android operating systems like GrapheneOS. Critics argued it undermines competition by effectively requiring developers to rely on Google's proprietary services, strengthening its monopoly over the Android ecosystem and disadvantaging alternative, privacy-focused operating systems. Users have also developed tools, such as the Play Integrity Fix module for Magisk/KernelSU/APatch, which tricks the attestation using leaked fingerprints of vulnerable devices. Furthermore, some have questioned the effectiveness of the attestation, claiming it does not deliver the level of security promised by Google and instead serves more as a form of vendor lock-in than a meaningful security measure. Activists have also raised concerns that it may violate antitrust and competition laws, like the Digital Markets Act.

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  • Computational learning theory

    Computational learning theory

    In computer science, computational learning theory (or just learning theory) is a subfield of artificial intelligence devoted to studying the design and analysis of machine learning algorithms. == Overview == Theoretical results in machine learning often focus on a type of inductive learning known as supervised learning. In supervised learning, an algorithm is provided with labeled samples. For instance, the samples might be descriptions of mushrooms, with labels indicating whether they are edible or not. The algorithm uses these labeled samples to create a classifier. This classifier assigns labels to new samples, including those it has not previously encountered. The goal of the supervised learning algorithm is to optimize performance metrics, such as minimizing errors on new samples. In addition to performance bounds, computational learning theory studies the time complexity and feasibility of learning . In computational learning theory, a computation is considered feasible if it can be done in polynomial time . There are two kinds of time complexity results: Positive results – Showing that a certain class of functions is learnable in polynomial time. Negative results – Showing that certain classes cannot be learned in polynomial time. Negative results often rely on commonly believed, but yet unproven assumptions, such as: Computational complexity – P ≠ NP (the P versus NP problem); Cryptographic – One-way functions exist. There are several different approaches to computational learning theory based on making different assumptions about the inference principles used to generalise from limited data. This includes different definitions of probability (see frequency probability, Bayesian probability) and different assumptions on the generation of samples. The different approaches include: Exact learning, proposed by Dana Angluin; Probably approximately correct learning (PAC learning), proposed by Leslie Valiant; VC theory, proposed by Vladimir Vapnik and Alexey Chervonenkis; Inductive inference as developed by Ray Solomonoff; Algorithmic learning theory, from the work of E. Mark Gold; Online machine learning, from the work of Nick Littlestone. While its primary goal is to understand learning abstractly, computational learning theory has led to the development of practical algorithms. For example, PAC theory inspired boosting, VC theory led to support vector machines, and Bayesian inference led to belief networks.

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  • Prefrontal cortex basal ganglia working memory

    Prefrontal cortex basal ganglia working memory

    Prefrontal cortex basal ganglia working memory (PBWM) is an algorithm that models working memory in the prefrontal cortex and the basal ganglia. It can be compared to long short-term memory (LSTM) in functionality, but is more biologically explainable. It uses the primary value learned value model to train prefrontal cortex working-memory updating system, based on the biology of the prefrontal cortex and basal ganglia. It is used as part of the Leabra framework and was implemented in Emergent in 2019. == Abstract == The prefrontal cortex has long been thought to subserve both working memory (the holding of information online for processing) and "executive" functions (deciding how to manipulate working memory and perform processing). Although many computational models of working memory have been developed, the mechanistic basis of executive function remains elusive. PBWM is a computational model of the prefrontal cortex to control both itself and other brain areas in a strategic, task-appropriate manner. These learning mechanisms are based on subcortical structures in the midbrain, basal ganglia and amygdala, which together form an actor/critic architecture. The critic system learns which prefrontal representations are task-relevant and trains the actor, which in turn provides a dynamic gating mechanism for controlling working memory updating. Computationally, the learning mechanism is designed to simultaneously solve the temporal and structural credit assignment problems. The model's performance compares favorably with standard backpropagation-based temporal learning mechanisms on the challenging 1-2-AX working memory task, and other benchmark working memory tasks. == Model == First, there are multiple separate stripes (groups of units) in the prefrontal cortex and striatum layers. Each stripe can be independently updated, such that this system can remember several different things at the same time, each with a different "updating policy" of when memories are updated and maintained. The active maintenance of the memory is in prefrontal cortex (PFC), and the updating signals (and updating policy more generally) come from the striatum units (a subset of basal ganglia units). PVLV provides reinforcement learning signals to train up the dynamic gating system in the basal ganglia. === Sensory input and motor output === The sensory input is connected to the posterior cortex which is connected to the motor output. The sensory input is also linked to the PVLV system. === Posterior cortex === The posterior cortex form the hidden layers of the input/output mapping. The PFC is connected with the posterior cortex to contextualize this input/output mapping. === PFC === The PFC (for output gating) has a localist one-to-one representation of the input units for every stripe. Thus, you can look at these PFC representations and see directly what the network is maintaining. The PFC maintains the working memory needed to perform the task. === Striatum === This is the dynamic gating system representing the striatum units of the basal ganglia. Every even-index unit within a stripe represents "Go", while the odd-index units represent "NoGo." The Go units cause updating of the PFC, while the NoGo units cause the PFC to maintain its existing memory representation. There are groups of units for every stripe. In the PBWM model in Emergent, the matrices represent the striatum. === PVLV === All of these layers are part of PVLV system. The PVLV system controls the dopaminergic modulation of the basal ganglia (BG). Thus, BG/PVLV form an actor-critic architecture where the PVLV system learns when to update. ==== SNrThal ==== SNrThal represents the substantia nigra pars reticulata (SNr) and the associated area of the thalamus, which produce a competition among the Go/NoGo units within a given stripe and mediates competition using k-winners-take-all dynamics. If there is more overall Go activity in a given stripe, then the associated SNrThal unit gets activated, and it drives updating in PFC. For every stripe, there is one unit in SNrThal. ==== VTA and SNc ==== Ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) are part of the dopamine layer. This layer models midbrain dopamine neurons. They control the dopaminergic modulation of the basal ganglia.

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  • Synaptic transistor

    Synaptic transistor

    A synaptic transistor is an electrical device that can learn in ways similar to a neural synapse. It optimizes its own properties for the functions it has carried out in the past. The device mimics the behavior of the property of neurons called spike-timing-dependent plasticity, or STDP. == Structure == Its structure is similar to that of a field effect transistor, where an ionic liquid takes the place of the gate insulating layer between the gate electrode and the conducting channel. That channel is composed of samarium nickelate (SmNiO3, or SNO) rather than the field effect transistor's doped silicon. == Function == A synaptic transistor has a traditional immediate response whose amount of current that passes between the source and drain contacts varies with voltage applied to the gate electrode. It also produces a much slower learned response such that the conductivity of the SNO layer varies in response to the transistor's STDP history, essentially by shuttling oxygen ions between the SNO and the ionic liquid. The analog of strengthening a synapse is to increase the SNO's conductivity, which essentially increases gain. Similarly, weakening a synapse is analogous to decreasing the SNO's conductivity, lowering the gain. The input and output of the synaptic transistor are continuous analog values, rather than digital on-off signals. While the physical structure of the device has the potential to learn from history, it contains no way to bias the transistor to control the memory effect. An external supervisory circuit converts the time delay between input and output into a voltage applied to the ionic liquid that either drives ions into the SNO or removes them. A network of such devices can learn particular responses to "sensory inputs", with those responses being learned through experience rather than explicitly programmed.

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  • Cygwin

    Cygwin

    Cygwin ( SIG-win) is a free and open-source Unix-like environment and command-line interface (CLI) for Microsoft Windows. The project also provides a software repository containing open-source packages. Cygwin allows source code for Unix-like operating systems to be compiled and run on Windows. Cygwin provides native integration of Windows-based applications. The terminal emulator mintty is the default command-line interface provided to interact with the environment. The Cygwin installation directory layout mimics the root file system of Unix-like systems, with directories such as /bin, /home, /etc, /usr, and /var. Cygwin is released under the GNU Lesser General Public License version 3. It was originally developed by Cygnus Solutions, which was later acquired by Red Hat (now part of IBM), to port the GNU toolchain to Win32, including the GNU Compiler Suite. Rather than rewrite the tools to use the Win32 runtime environment, Cygwin implemented a POSIX-compatible environment in the form of a DLL. The brand motto is "Get that Linux feeling – on Windows", although Cygwin doesn't have Linux in it. == History == Cygwin began in 1995 as a project of Steve Chamberlain, a Cygnus engineer who observed that Windows NT and 95 used COFF as their object file format, and that GNU already included support for x86 and COFF, and the C library newlib. He thought that it would be possible to retarget GCC and produce a cross compiler generating executables that could run on Windows. A prototype was later developed. Chamberlain bootstrapped the compiler on a Windows system, to emulate Unix to let the GNU configure shell script run. Initially, Cygwin was called Cygwin32. When Microsoft registered the trademark Win32, the "32" was dropped to simply become Cygwin. In 1999, Cygnus offered Cygwin 1.0 as a commercial product. Subsequent versions have not been released, instead relying on continued open source releases. Geoffrey Noer was the project lead from 1996 to 1999. Christopher Faylor was lead from 1999 to 2004; he left Red Hat and became co-lead with Corinna Vinschen. Corinna Vinschen has been the project lead from mid-2014 to date (as of September, 2024). From June 23, 2016, the Cygwin library version 2.5.2 was licensed under the GNU Lesser General Public License (LGPL) version 3. == Description == Cygwin is provided in two versions: the full 64-bit version and a stripped-down 32-bit version, whose final version was released in 2022. Cygwin consists of a library that implements the POSIX system call API in terms of Windows system calls to enable the running of a large number of application programs equivalent to those on Unix systems, and a GNU development toolchain (including GCC and GDB). Programmers have ported the X Window System, K Desktop Environment 3, GNOME, Apache, and TeX. Cygwin permits installing inetd, syslogd, sshd, Apache, and other daemons as standard Windows services. Cygwin programs have full access to the Windows API and other Windows libraries. Cygwin programs are installed by running Cygwin's "setup" program, which downloads them from repositories on the Internet. The Cygwin API library is licensed under the GNU Lesser General Public License version 3 (or later), with an exception to allow linking to any free and open-source software whose license conforms to the Open Source Definition. Cygwin consists of two parts: A dynamic-link library in the form of a C standard library that acts as a compatibility layer for the POSIX API and A collection of software tools and applications that provide a Unix-like look and feel. Cygwin supports POSIX symbolic links, representing them as plain-text files with the system attribute set. Cygwin 1.5 represented them as Windows Explorer shortcuts, but this was changed for reasons of performance and POSIX correctness. Cygwin also recognises NTFS junction points and symbolic links and treats them as POSIX symbolic links, but it does not create them. The POSIX API for handling access control lists (ACLs) is supported. === Technical details === A Cygwin-specific version of the Unix mount command allows mounting Windows paths as "filesystems" in the Unix file space. Initial mount points can be configured in /etc/fstab, which has a format very similar to Unix systems, except that Windows paths appear in place of devices. Filesystems can be mounted in binary mode (by default), or in text mode, which enables automatic conversion between LF and CRLF endings (which only affects programs that open files without explicitly specifying text or binary mode). Cygwin 1.7 introduced comprehensive support for POSIX locales, and the UTF-8 Unicode encoding became the default. The fork system call for duplicating a process is fully implemented, but the copy-on-write optimization strategy could not be used. Cygwin's default user interface is the bash shell running in the mintty terminal emulator. The DLL also implements pseudo terminal (pty) devices, and Cygwin ships with a number of terminal emulators that are based on them, including rxvt/urxvt and xterm. The version of GCC that comes with Cygwin has various extensions for creating Windows DLLs, such as specifying whether a program is a windowing or console-mode program. Support for compiling programs that do not require the POSIX compatibility layer provided by the Cygwin DLL used to be included in the default GCC, but as of 2014, it is provided by cross-compilers contributed by the MinGW-w64 project. == Software packages == Cygwin's base package selection is approximately 100MB, containing the bash (interactive user) and dash (installation) shells and the core file and text manipulation utilities. Additional packages are available as optional installs from within the Cygwin "setup" program and package manager ("setup-x86_64.exe" – 64 bit). The Cygwin Ports project provided additional packages that were not available in the Cygwin distribution itself. Examples included GNOME, K Desktop Environment 3, MySQL database, and the PHP scripting language. Most ports have been adopted by volunteer maintainers as Cygwin packages, and Cygwin Ports are no longer maintained. Cygwin ships with GTK+ and Qt. The Cygwin/X project allows graphical Unix programs to display their user interfaces on the Windows desktop for both local and remote programs.

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  • Operational taxonomic unit

    Operational taxonomic unit

    An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).

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  • Diffusion map

    Diffusion map

    Diffusion maps is a dimensionality reduction or feature extraction algorithm introduced by Coifman and Lafon which computes a family of embeddings of a data set into Euclidean space (often low-dimensional) whose coordinates can be computed from the eigenvectors and eigenvalues of a diffusion operator on the data. The Euclidean distance between points in the embedded space is equal to the "diffusion distance" between probability distributions centered at those points. Different from linear dimensionality reduction methods such as principal component analysis (PCA), diffusion maps are part of the family of nonlinear dimensionality reduction methods which focus on discovering the underlying manifold that the data has been sampled from. By integrating local similarities at different scales, diffusion maps give a global description of the data-set. Compared with other methods, the diffusion map algorithm is robust to noise perturbation and computationally inexpensive. == Definition of diffusion maps == Following and , diffusion maps can be defined in four steps. === Connectivity === Diffusion maps exploit the relationship between heat diffusion and random walk Markov chain. The basic observation is that if we take a random walk on the data, walking to a nearby data-point is more likely than walking to another that is far away. Let ( X , A , μ ) {\displaystyle (X,{\mathcal {A}},\mu )} be a measure space, where X {\displaystyle X} is the data set and μ {\displaystyle \mu } represents the distribution of the points on X {\displaystyle X} . Based on this, the connectivity k {\displaystyle k} between two data points, x {\displaystyle x} and y {\displaystyle y} , can be defined as the probability of walking from x {\displaystyle x} to y {\displaystyle y} in one step of the random walk. Usually, this probability is specified in terms of a kernel function of the two points: k : X × X → R {\displaystyle k:X\times X\rightarrow \mathbb {R} } . For example, the popular Gaussian kernel: k ( x , y ) = exp ⁡ ( − | | x − y | | 2 ϵ ) {\displaystyle k(x,y)=\exp \left(-{\frac {||x-y||^{2}}{\epsilon }}\right)} More generally, the kernel function has the following properties k ( x , y ) = k ( y , x ) {\displaystyle k(x,y)=k(y,x)} ( k {\displaystyle k} is symmetric) k ( x , y ) ≥ 0 ∀ x , y {\displaystyle k(x,y)\geq 0\,\,\forall x,y} ( k {\displaystyle k} is positivity preserving). The kernel constitutes the prior definition of the local geometry of the data-set. Since a given kernel will capture a specific feature of the data set, its choice should be guided by the application that one has in mind. This is a major difference with methods such as principal component analysis, where correlations between all data points are taken into account at once. Given ( X , k ) {\displaystyle (X,k)} , we can then construct a reversible discrete-time Markov chain on X {\displaystyle X} (a process known as the normalized graph Laplacian construction): d ( x ) = ∫ X k ( x , y ) d μ ( y ) {\displaystyle d(x)=\int _{X}k(x,y)d\mu (y)} and define: p ( x , y ) = k ( x , y ) d ( x ) {\displaystyle p(x,y)={\frac {k(x,y)}{d(x)}}} Although the new normalized kernel does not inherit the symmetric property, it does inherit the positivity-preserving property and gains a conservation property: ∫ X p ( x , y ) d μ ( y ) = 1 {\displaystyle \int _{X}p(x,y)d\mu (y)=1} === Diffusion process === From p ( x , y ) {\displaystyle p(x,y)} we can construct a transition matrix of a Markov chain ( M {\displaystyle M} ) on X {\displaystyle X} . In other words, p ( x , y ) {\displaystyle p(x,y)} represents the one-step transition probability from x {\displaystyle x} to y {\displaystyle y} , and M t {\displaystyle M^{t}} gives the t-step transition matrix. We define the diffusion matrix L {\displaystyle L} (it is also a version of graph Laplacian matrix) L i , j = k ( x i , x j ) {\displaystyle L_{i,j}=k(x_{i},x_{j})\,} We then define the new kernel L i , j ( α ) = k ( α ) ( x i , x j ) = L i , j ( d ( x i ) d ( x j ) ) α {\displaystyle L_{i,j}^{(\alpha )}=k^{(\alpha )}(x_{i},x_{j})={\frac {L_{i,j}}{(d(x_{i})d(x_{j}))^{\alpha }}}\,} or equivalently, L ( α ) = D − α L D − α {\displaystyle L^{(\alpha )}=D^{-\alpha }LD^{-\alpha }\,} where D is a diagonal matrix and D i , i = ∑ j L i , j . {\displaystyle D_{i,i}=\sum _{j}L_{i,j}.} We apply the graph Laplacian normalization to this new kernel: M = ( D ( α ) ) − 1 L ( α ) , {\displaystyle M=({D}^{(\alpha )})^{-1}L^{(\alpha )},\,} where D ( α ) {\displaystyle D^{(\alpha )}} is a diagonal matrix and D i , i ( α ) = ∑ j L i , j ( α ) . {\displaystyle {D}_{i,i}^{(\alpha )}=\sum _{j}L_{i,j}^{(\alpha )}.} p ( x j , t | x i ) = M i , j t {\displaystyle p(x_{j},t|x_{i})=M_{i,j}^{t}\,} One of the main ideas of the diffusion framework is that running the chain forward in time (taking larger and larger powers of M {\displaystyle M} ) reveals the geometric structure of X {\displaystyle X} at larger and larger scales (the diffusion process). Specifically, the notion of a cluster in the data set is quantified as a region in which the probability of escaping this region is low (within a certain time t). Therefore, t not only serves as a time parameter, but it also has the dual role of scale parameter. The eigendecomposition of the matrix M t {\displaystyle M^{t}} yields M i , j t = ∑ l λ l t ψ l ( x i ) ϕ l ( x j ) {\displaystyle M_{i,j}^{t}=\sum _{l}\lambda _{l}^{t}\psi _{l}(x_{i})\phi _{l}(x_{j})\,} where { λ l } {\displaystyle \{\lambda _{l}\}} is the sequence of eigenvalues of M {\displaystyle M} and { ψ l } {\displaystyle \{\psi _{l}\}} and { ϕ l } {\displaystyle \{\phi _{l}\}} are the biorthogonal left and right eigenvectors respectively. Due to the spectrum decay of the eigenvalues, only a few terms are necessary to achieve a given relative accuracy in this sum. ==== Parameter α and the diffusion operator ==== The reason to introduce the normalization step involving α {\displaystyle \alpha } is to tune the influence of the data point density on the infinitesimal transition of the diffusion. In some applications, the sampling of the data is generally not related to the geometry of the manifold we are interested in describing. In this case, we can set α = 1 {\displaystyle \alpha =1} and the diffusion operator approximates the Laplace–Beltrami operator. We then recover the Riemannian geometry of the data set regardless of the distribution of the points. To describe the long-term behavior of the point distribution of a system of stochastic differential equations, we can use α = 0.5 {\displaystyle \alpha =0.5} and the resulting Markov chain approximates the Fokker–Planck diffusion. With α = 0 {\displaystyle \alpha =0} , it reduces to the classical graph Laplacian normalization. === Diffusion distance === The diffusion distance at time t {\displaystyle t} between two points can be measured as the similarity of two points in the observation space with the connectivity between them. It is given by D t ( x i , x j ) 2 = ∑ y ( p ( y , t | x i ) − p ( y , t | x j ) ) 2 ϕ 0 ( y ) {\displaystyle D_{t}(x_{i},x_{j})^{2}=\sum _{y}{\frac {(p(y,t|x_{i})-p(y,t|x_{j}))^{2}}{\phi _{0}(y)}}} where ϕ 0 ( y ) {\displaystyle \phi _{0}(y)} is the stationary distribution of the Markov chain, given by the first left eigenvector of M {\displaystyle M} . Explicitly: ϕ 0 ( y ) = d ( y ) ∑ z ∈ X d ( z ) {\displaystyle \phi _{0}(y)={\frac {d(y)}{\sum _{z\in X}d(z)}}} Intuitively, D t ( x i , x j ) {\displaystyle D_{t}(x_{i},x_{j})} is small if there is a large number of short paths connecting x i {\displaystyle x_{i}} and x j {\displaystyle x_{j}} . There are several interesting features associated with the diffusion distance, based on our previous discussion that t {\displaystyle t} also serves as a scale parameter: Points are closer at a given scale (as specified by D t ( x i , x j ) {\displaystyle D_{t}(x_{i},x_{j})} ) if they are highly connected in the graph, therefore emphasizing the concept of a cluster. This distance is robust to noise, since the distance between two points depends on all possible paths of length t {\displaystyle t} between the points. From a machine learning point of view, the distance takes into account all evidences linking x i {\displaystyle x_{i}} to x j {\displaystyle x_{j}} , allowing us to conclude that this distance is appropriate for the design of inference algorithms based on the majority of preponderance. === Diffusion process and low-dimensional embedding === The diffusion distance can be calculated using the eigenvectors by D t ( x i , x j ) 2 = ∑ l λ l 2 t ( ψ l ( x i ) − ψ l ( x j ) ) 2 {\displaystyle D_{t}(x_{i},x_{j})^{2}=\sum _{l}\lambda _{l}^{2t}(\psi _{l}(x_{i})-\psi _{l}(x_{j}))^{2}\,} So the eigenvectors can be used as a new set of coordinates for the data. The diffusion map is defined as: Ψ t ( x ) = ( λ 1 t ψ 1 ( x ) , λ 2 t ψ 2 ( x ) , … , λ k t ψ k ( x ) ) {\displaystyle \Psi _{t}(x)=(\lambda _{1}^{t}\psi _{1}(x),\lambda _{2}^{t}\psi _{2}(x),\ld

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