Hugging Face, Inc., is an American company based in New York City that develops computation tools for building applications using machine learning. Its transformers library built for natural language processing applications and its platform allow users to share machine learning models and datasets and showcase their work. == History == === Founding === The company was founded in 2016 by French entrepreneurs Clément Delangue, Julien Chaumond, and Thomas Wolf in New York City, originally as a company that developed a chatbot app targeted at teenagers. The company was named after the U+1F917 🤗 HUGGING FACE emoji. After open sourcing the model behind the chatbot, the company pivoted to focus on being a platform for machine learning. === AI boom === On April 28, 2021, the company launched the BigScience Research Workshop in collaboration with several other research groups to release an open large language model. In 2022, the workshop concluded with the announcement of BLOOM, a multilingual large language model with 176 billion parameters. In February 2023, the company announced partnership with Amazon Web Services (AWS) which would allow Hugging Face's products to be available to AWS customers to use them as the building blocks for their custom applications. The company also said the next generation of BLOOM will be run on Trainium, a proprietary machine learning chip created by AWS. In June 2024, the company announced, along with Meta and Scaleway, their launch of a new AI accelerator program for European startups. The initiative aimed to help startups integrate open foundation models into their products, accelerating the EU AI ecosystem. The program, based at STATION F in Paris, ran from September 2024 to February 2025. Selected startups received mentoring, and access to AI models and tools and Scaleway's computing power. On September 23, 2024, to further the International Decade of Indigenous Languages, Hugging Face teamed up with Meta and UNESCO to launch a new online language translator. It was built on Meta's No Language Left Behind open-source AI model, enabling free text translation across 200 languages, including many low-resource languages. In April 2025, Hugging Face announced that they acquired a humanoid robotics startup, Pollen Robotics, based in France and founded by Matthieu Lapeyre and Pierre Rouanet in 2016. In an X tweet, Delangue shared his vision to "make Artificial Intelligence robotics Open Source". === Cyberattacks === In early 2026, hackers hijacked the Hugging Face platform to launch Android-targeted attacks involving "powerful malware" which could completely take over a compromised target.
1 Second Everyday
1 Second Everyday (1SE) is an application developed by Cesar Kuriyama. The application allows the user to record one second of video every day and then chronologically edits (mashes) them together into a single film. It is compatible with iOS and Android. The idea of the application was developed by Kuriyama's 1 Second Everyday — Age 30 video. The application was launched in January 2013. 1 Second Everyday played a part in the plot of Chef and also became the inspiration for the 2014 short animated clip Feast. == Background == === Kuriyama's video === In February 2011, when Cesar Kuriyama turned 30, after saving money, he quit his job in an advertising firm and took a year off to travel. During this time, he started working on a project he called 1 Second Everyday. As part of the project, every day he recorded one second of video – something that was supposed to help him remember that day. He started the project because he was frustrated with his memory. He planned to stockpile the 365 one-second clips into one film to serve as a memento of his year. While working on the project Kuriyama realized that recording one second every day impacted the decisions he made in a positive way. After a year he made a 365-second clip out of his recordings. The video called 1 Second Everyday – Age 30, went viral. According to Kuriyama, he was initially inspired to take a year off from work by a TED talk given by Stefan Sagmeister called "The Power of Time Off." Kuriyama also delivered a TED talk about 1 Second Everyday in 2012 at TED 2012 in Long Beach California. === Kickstarter campaign === After completing his own video, Kuriyama decided to develop an application that would allow the users to record one second every day and compile their own videos. He developed a prototype of the application and then in 2012, he launched a Kickstarter campaign to raise funds for completing the application. The campaign became one of the most backed app campaigns in the history of Kickstarter. It was backed by 11,281 backers who pledged a total of $56,959 on an initial goal of $20,000. Following the completion of the Kickstarter campaign, he partnered with an application design studio in Brooklyn to develop the application. 1 Second Everyday was released two weeks after the completion of its Kickstarter campaign. == Application == The application was released for iOS on 10 January 2013. An Android-compatible version of the application was developed later. Using it, the user can record the videos in the application or they can select one second portions from their libraries. 1 Second Everyday dates every snippet. The user can also set alarms to remember to record their daily video. In order to compile a video, the user selects the seconds they want and the application creates a compilation video. The user can keep multiple timelines. It also allows users to post directly on social networks. The main interface in 1 Second Everyday is a calendar, which shows the user which days have snippets and which they can still fill in. In the beginning, 1 Second Everyday restricted the recording to one second. However, the developers later released Super Seconds, which allowed users to record an additional half a second video. In 2014, 1 Second Everyday Crowds was launched, which is an area in the application featuring compilations of second clips from different users. == In the media == The Kickstarter campaign of 1 Second Everyday was featured in Entrepreneur's 3 Innovative Tech Startups on Kickstarter Right Now in 2012. The application was featured in The New York Times, The Washington Post, Gawker and other media outlets. By the end of the launch day, it was in Top 10 Free Apps on App Store. It was also selected as the App of the Week on GeekWire in 2013. Several other one-second compilation videos were also posted on the Internet after Kuriyama's video gained media attention. Sam Cornwell, an English photographer documented his son Indigo's growth using a montage of one-second iPhone clips. He shot these clips every single day from the moment of birth right up to the baby's first birthday. According to Cornwell, he was inspired by Kuriyama's project. The video of Cornwell's son gained considerable media attention after it was posted on YouTube. Save the Children also made a video commercial based on a similar format that showed a British girl oblivious of the Syrian war end up being a refugee. 1SE was a finalist for the Fast Company Innovation by Design Award in 2015, but lost to Google Maps. In 2015, Google Android created a gallery, Leap Second 2015, with the help of Droga5 and Kuriyama. The gallery showcased how people around the world enjoyed the one extra second of their lives. Through the 1 Second Everyday app available at Google Play, people were able to submit their extra second, which were then vetted and added to the gallery. The viewers were able to view other celebratory seconds from around the world as well as searching for them using different hashtags.
Vanishing gradient problem
In machine learning, the vanishing gradient problem is the problem of greatly diverging gradient magnitudes between earlier and later layers encountered when training neural networks with backpropagation. In such methods, neural network weights are updated proportional to their partial derivative of the loss function. As the number of forward propagation steps in a network increases, for instance due to greater network depth, the gradients of earlier weights are calculated with increasingly many multiplications. These multiplications shrink the gradient magnitude. Consequently, the gradients of earlier weights will be exponentially smaller than the gradients of later weights. This difference in gradient magnitude might introduce instability in the training process, slow it, or halt it entirely. For instance, consider the hyperbolic tangent activation function. The gradients of this function are in range [0,1]. The product of repeated multiplication with such gradients decreases exponentially. The inverse problem, when weight gradients at earlier layers get exponentially larger, is called the exploding gradient problem. Backpropagation allowed researchers to train supervised deep artificial neural networks from scratch, initially with little success. Hochreiter's diplom thesis of 1991 formally identified the reason for this failure in the "vanishing gradient problem", which not only affects many-layered feedforward networks, but also recurrent networks. The latter are trained by unfolding them into very deep feedforward networks, where a new layer is created for each time-step of an input sequence processed by the network (the combination of unfolding and backpropagation is termed backpropagation through time). == Prototypical models == This section is based on the paper On the difficulty of training Recurrent Neural Networks by Pascanu, Mikolov, and Bengio. === Recurrent network model === A generic recurrent network has hidden states h 1 , h 2 , … {\displaystyle h_{1},h_{2},\dots } , inputs u 1 , u 2 , … {\displaystyle u_{1},u_{2},\dots } , and outputs x 1 , x 2 , … {\displaystyle x_{1},x_{2},\dots } . Let it be parameterized by θ {\displaystyle \theta } , so that the system evolves as ( h t , x t ) = F ( h t − 1 , u t , θ ) {\displaystyle (h_{t},x_{t})=F(h_{t-1},u_{t},\theta )} Often, the output x t {\displaystyle x_{t}} is a function of h t {\displaystyle h_{t}} , as some x t = G ( h t ) {\displaystyle x_{t}=G(h_{t})} . The vanishing gradient problem already presents itself clearly when x t = h t {\displaystyle x_{t}=h_{t}} , so we simplify our notation to the special case with: x t = F ( x t − 1 , u t , θ ) {\displaystyle x_{t}=F(x_{t-1},u_{t},\theta )} Now, take its differential: d x t = ∇ θ F ( x t − 1 , u t , θ ) d θ + ∇ x F ( x t − 1 , u t , θ ) d x t − 1 = ∇ θ F ( x t − 1 , u t , θ ) d θ + ∇ x F ( x t − 1 , u t , θ ) [ ∇ θ F ( x t − 2 , u t − 1 , θ ) d θ + ∇ x F ( x t − 2 , u t − 1 , θ ) d x t − 2 ] ⋮ = [ ∇ θ F ( x t − 1 , u t , θ ) + ∇ x F ( x t − 1 , u t , θ ) ∇ θ F ( x t − 2 , u t − 1 , θ ) + ⋯ ] d θ {\displaystyle {\begin{aligned}dx_{t}&=\nabla _{\theta }F(x_{t-1},u_{t},\theta )d\theta +\nabla _{x}F(x_{t-1},u_{t},\theta )dx_{t-1}\\&=\nabla _{\theta }F(x_{t-1},u_{t},\theta )d\theta +\nabla _{x}F(x_{t-1},u_{t},\theta )\left[\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )d\theta +\nabla _{x}F(x_{t-2},u_{t-1},\theta )dx_{t-2}\right]\\&\;\;\vdots \\&=\left[\nabla _{\theta }F(x_{t-1},u_{t},\theta )+\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )+\cdots \right]d\theta \end{aligned}}} Training the network requires us to define a loss function to be minimized. Let it be L ( x T , u 1 , … , u T ) {\displaystyle L(x_{T},u_{1},\dots ,u_{T})} , then minimizing it by gradient descent gives Δ θ = − η ⋅ [ ∇ x L ( x T ) ( ∇ θ F ( x t − 1 , u t , θ ) + ∇ x F ( x t − 1 , u t , θ ) ∇ θ F ( x t − 2 , u t − 1 , θ ) + ⋯ ) ] T {\displaystyle \Delta \theta =-\eta \cdot \left[\nabla _{x}L(x_{T})\left(\nabla _{\theta }F(x_{t-1},u_{t},\theta )+\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )+\cdots \right)\right]^{T}} where η {\displaystyle \eta } is the learning rate. The vanishing/exploding gradient problem appears because there are repeated multiplications, of the form ∇ x F ( x t − 1 , u t , θ ) ∇ x F ( x t − 2 , u t − 1 , θ ) ∇ x F ( x t − 3 , u t − 2 , θ ) ⋯ {\displaystyle \nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{x}F(x_{t-2},u_{t-1},\theta )\nabla _{x}F(x_{t-3},u_{t-2},\theta )\cdots } ==== Example: recurrent network with sigmoid activation ==== For a concrete example, consider a typical recurrent network defined by x t = F ( x t − 1 , u t , θ ) = W rec σ ( x t − 1 ) + W in u t + b {\displaystyle x_{t}=F(x_{t-1},u_{t},\theta )=W_{\text{rec}}\sigma (x_{t-1})+W_{\text{in}}u_{t}+b} where θ = ( W rec , W in ) {\displaystyle \theta =(W_{\text{rec}},W_{\text{in}})} is the network parameter, σ {\displaystyle \sigma } is the sigmoid activation function, applied to each vector coordinate separately, and b {\displaystyle b} is the bias vector. Then, ∇ x F ( x t − 1 , u t , θ ) = W rec diag ( σ ′ ( x t − 1 ) ) {\displaystyle \nabla _{x}F(x_{t-1},u_{t},\theta )=W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-1}))} , and so ∇ x F ( x t − 1 , u t , θ ) ∇ x F ( x t − 2 , u t − 1 , θ ) ⋯ ∇ x F ( x t − k , u t − k + 1 , θ ) = W rec diag ( σ ′ ( x t − 1 ) ) W rec diag ( σ ′ ( x t − 2 ) ) ⋯ W rec diag ( σ ′ ( x t − k ) ) {\displaystyle {\begin{aligned}&\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{x}F(x_{t-2},u_{t-1},\theta )\cdots \nabla _{x}F(x_{t-k},u_{t-k+1},\theta )\\&=W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-1}))W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-2}))\cdots W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-k}))\end{aligned}}} Since | σ ′ | ≤ 1 {\displaystyle \left|\sigma '\right|\leq 1} , the operator norm of the above multiplication is bounded above by ‖ W rec ‖ k {\displaystyle \left\|W_{\text{rec}}\right\|^{k}} . So if the spectral radius of W rec {\displaystyle W_{\text{rec}}} is γ < 1 {\displaystyle \gamma <1} , then at large k {\displaystyle k} , the above multiplication has operator norm bounded above by γ k → 0 {\displaystyle \gamma ^{k}\to 0} . This is the prototypical vanishing gradient problem. The effect of a vanishing gradient is that the network cannot learn long-range effects. Recall Equation (loss differential): ∇ θ L = ∇ x L ( x T , u 1 , … , u T ) [ ∇ θ F ( x t − 1 , u t , θ ) + ∇ x F ( x t − 1 , u t , θ ) ∇ θ F ( x t − 2 , u t − 1 , θ ) + ⋯ ] {\displaystyle \nabla _{\theta }L=\nabla _{x}L(x_{T},u_{1},\dots ,u_{T})\left[\nabla _{\theta }F(x_{t-1},u_{t},\theta )+\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )+\cdots \right]} The components of ∇ θ F ( x , u , θ ) {\displaystyle \nabla _{\theta }F(x,u,\theta )} are just components of σ ( x ) {\displaystyle \sigma (x)} and u {\displaystyle u} , so if u t , u t − 1 , … {\displaystyle u_{t},u_{t-1},\dots } are bounded, then ‖ ∇ θ F ( x t − k − 1 , u t − k , θ ) ‖ {\displaystyle \left\|\nabla _{\theta }F(x_{t-k-1},u_{t-k},\theta )\right\|} is also bounded by some M > 0 {\displaystyle M>0} , and so the terms in ∇ θ L {\displaystyle \nabla _{\theta }L} decay as M γ k {\displaystyle M\gamma ^{k}} . This means that, effectively, ∇ θ L {\displaystyle \nabla _{\theta }L} is affected only by the first O ( γ − 1 ) {\displaystyle O(\gamma ^{-1})} terms in the sum. If γ ≥ 1 {\displaystyle \gamma \geq 1} , the above analysis does not quite work. For the prototypical exploding gradient problem, the next model is clearer. === Dynamical systems model === Following (Doya, 1993), consider this one-neuron recurrent network with sigmoid activation: x t + 1 = ( 1 − ε ) x t + ε σ ( w x t + b ) + ε w ′ u t {\displaystyle x_{t+1}=(1-\varepsilon )x_{t}+\varepsilon \sigma (wx_{t}+b)+\varepsilon w'u_{t}} At the small ε {\displaystyle \varepsilon } limit, the dynamics of the network becomes d x d t = − x ( t ) + σ ( w x ( t ) + b ) + w ′ u ( t ) {\displaystyle {\frac {dx}{dt}}=-x(t)+\sigma (wx(t)+b)+w'u(t)} Consider first the autonomous case, with u = 0 {\displaystyle u=0} . Set w = 5.0 {\displaystyle w=5.0} , and vary b {\displaystyle b} in [ − 3 , − 2 ] {\displaystyle [-3,-2]} . As b {\displaystyle b} decreases, the system has 1 stable point, then has 2 stable points and 1 unstable point, and finally has 1 stable point again. Explicitly, the stable points are ( x , b ) = ( x , ln ( x 1 − x ) − 5 x ) {\displaystyle (x,b)=\left(x,\ln \left({\frac {x}{1-x}}\right)-5x\right)} . Now consider Δ x ( T ) Δ x ( 0 ) {\displaystyle {\frac {\Delta x(T)}{\Delta x(0)}}} and Δ x ( T ) Δ b {\displaystyle {\frac {\Delta x(T)}{\Delta b}}} , where T {\displaystyle T} is large enough that the system has settled into one of the stable points. If ( x ( 0 ) , b ) {\displaystyle (x(0),b)} puts the system very close to an unstable point, then a tiny variation in x ( 0 ) {\displaystyle x(0)} or b {\displaystyle b} wo
Markov model
In probability theory, a Markov model is a stochastic model used to model pseudo-randomly changing systems. It is assumed that future states depend only on the current state, not on the events that occurred before it (that is, it assumes the Markov property). Generally, this assumption enables reasoning and computation with the model that would otherwise be intractable. For this reason, in the fields of predictive modelling and probabilistic forecasting, it is desirable for a given model to exhibit the Markov property. == Introduction == Andrey Andreyevich Markov (14 June 1856 – 20 July 1922) was a Russian mathematician best known for his work on stochastic processes. A primary subject of his research later became known as the Markov chain. There are four common Markov models used in different situations, depending on whether every sequential state is observable or not, and whether the system is to be adjusted on the basis of observations made: == Markov chain == The simplest Markov model is the Markov chain. It models the state of a system with a random variable that changes through time. In this context, the Markov property indicates that the distribution for this variable depends only on the distribution of a previous state. An example use of a Markov chain is Markov chain Monte Carlo, which uses the Markov property to prove that a particular method for performing a random walk will sample from the joint distribution. == Hidden Markov model == A hidden Markov model is a Markov chain for which the state is only partially observable or noisily observable. In other words, observations are related to the state of the system, but they are typically insufficient to precisely determine the state. Several well-known algorithms for hidden Markov models exist. For example, given a sequence of observations, the Viterbi algorithm will compute the most-likely corresponding sequence of states, the forward algorithm will compute the probability of the sequence of observations, and the Baum–Welch algorithm will estimate the starting probabilities, the transition function, and the observation function of a hidden Markov model. One common use is for speech recognition, where the observed data is the speech audio waveform and the hidden state is the spoken text. In this example, the Viterbi algorithm finds the most likely sequence of spoken words given the speech audio. == Markov decision process == A Markov decision process is a Markov chain in which state transitions depend on the current state and an action vector that is applied to the system. Typically, a Markov decision process is used to compute a policy of actions that will maximize some utility with respect to expected rewards. == Partially observable Markov decision process == A partially observable Markov decision process (POMDP) is a Markov decision process in which the state of the system is only partially observed. POMDPs are known to be NP complete, but recent approximation techniques have made them useful for a variety of applications, such as controlling simple agents or robots. == Markov random field == A Markov random field, or Markov network, may be considered to be a generalization of a Markov chain in multiple dimensions. In a Markov chain, state depends only on the previous state in time, whereas in a Markov random field, each state depends on its neighbors in any of multiple directions. A Markov random field may be visualized as a field or graph of random variables, where the distribution of each random variable depends on the neighboring variables with which it is connected. More specifically, the joint distribution for any random variable in the graph can be computed as the product of the "clique potentials" of all the cliques in the graph that contain that random variable. Modeling a problem as a Markov random field is useful because it implies that the joint distributions at each vertex in the graph may be computed in this manner. == Hierarchical Markov models == Hierarchical Markov models can be applied to categorize human behavior at various levels of abstraction. For example, a series of simple observations, such as a person's location in a room, can be interpreted to determine more complex information, such as in what task or activity the person is performing. Two kinds of Hierarchical Markov Models are the Hierarchical hidden Markov model and the Abstract Hidden Markov Model. Both have been used for behavior recognition and certain conditional independence properties between different levels of abstraction in the model allow for faster learning and inference. == Tolerant Markov model == A Tolerant Markov model (TMM) is a probabilistic-algorithmic Markov chain model. It assigns the probabilities according to a conditioning context that considers the last symbol, from the sequence to occur, as the most probable instead of the true occurring symbol. A TMM can model three different natures: substitutions, additions or deletions. Successful applications have been efficiently implemented in DNA sequences compression. == Markov-chain forecasting models == Markov-chains have been used as a forecasting methods for several topics, for example price trends, wind power and solar irradiance. The Markov-chain forecasting models utilize a variety of different settings, from discretizing the time-series to hidden Markov-models combined with wavelets and the Markov-chain mixture distribution model (MCM).
Linear genetic programming
"Linear genetic programming" is unrelated to "linear programming". Linear genetic programming (LGP) is a particular method of genetic programming wherein computer programs in a population are represented as a sequence of register-based instructions from an imperative programming language or machine language. The adjective "linear" stems from the fact that each LGP program is a sequence of instructions and the sequence of instructions is normally executed sequentially. Like in other programs, the data flow in LGP can be modeled as a graph that will visualize the potential multiple usage of register contents and the existence of structurally noneffective code (introns) which are two main differences of this genetic representation from the more common tree-based genetic programming (TGP) variant. Like other Genetic Programming methods, Linear genetic programming requires the input of data to run the program population on. Then, the output of the program (its behaviour) is judged against some target behaviour, using a fitness function. However, LGP is generally more efficient than tree genetic programming due to its two main differences mentioned above: Intermediate results (stored in registers) can be reused and a simple intron removal algorithm exists that can be executed to remove all non-effective code prior to programs being run on the intended data. These two differences often result in compact solutions and substantial computational savings compared to the highly constrained data flow in trees and the common method of executing all tree nodes in TGP. Furthermore, LGP naturally has multiple outputs by defining multiple output registers and easily cooperates with control flow operations. Linear genetic programming has been applied in many domains, including system modeling and system control with considerable success. Linear genetic programming should not be confused with linear tree programs in tree genetic programming, program composed of a variable number of unary functions and a single terminal. Note that linear tree GP differs from bit string genetic algorithms since a population may contain programs of different lengths and there may be more than two types of functions or more than two types of terminals. == Examples of LGP programs == Because LGP programs are basically represented by a linear sequence of instructions, they are simpler to read and to operate on than their tree-based counterparts. For example, a simple program written to solve a Boolean function problem with 3 inputs (in R1, R2, R3) and one output (in R0), could read like this: R1, R2, R3 have to be declared as input (read-only) registers, while R0 and R4 are declared as calculation (read-write) registers. This program is very simple, having just 5 instructions. But mutation and crossover operators could work to increase the length of the program, as well as the content of each of its instructions. Note that one instruction is non-effective or an intron (marked), since it does not impact the output register R0. Recognition of those instructions is the basis for the intron removal algorithm which is used analyze code prior to execution. Technically, this happens by copying an individual and then run the intron removal once. The copy with removed introns is then executed as many times as dictated by the number of training cases. Notably, the original individual is left intact, so as to continue participating in the evolutionary process. It is only the copy that is executed that is compressed by removing these "structural" introns. Another simple program, this one written in the LGP language Slash/A looks like a series of instructions separated by a slash: By representing such code in bytecode format, i.e. as an array of bytes each representing a different instruction, one can make mutation operations simply by changing an element of such an array.
Aggregation (linguistics)
In linguistics, aggregation is a subtask of natural language generation, which involves merging syntactic constituents (such as sentences and phrases) together. Sometimes aggregation can be done at a conceptual level. == Examples == A simple example of syntactic aggregation is merging the two sentences John went to the shop and John bought an apple into the single sentence John went to the shop and bought an apple. Syntactic aggregation can be much more complex than this. For example, aggregation can embed one of the constituents in the other; e.g., we can aggregate John went to the shop and The shop was closed into the sentence John went to the shop, which was closed. From a pragmatic perspective, aggregating sentences together often suggests to the reader that these sentences are related to each other. If this is not the case, the reader may be confused. For example, someone who reads John went to the shop and bought an apple may infer that the apple was bought in the shop; if this is not the case, then these sentences should not be aggregated. == Algorithms and issues == Aggregation algorithms must do two things: Decide when two constituents should be aggregated Decide how two constituents should be aggregated, and create the aggregated structure The first issue, deciding when to aggregate, is poorly understood. Aggegration decisions certainly depend on the semantic relations between the constituents, as mentioned above; they also depend on the genre (e.g., bureaucratic texts tend to be more aggregated than instruction manuals). They probably should depend on rhetorical and discourse structure. The literacy level of the reader is also probably important (poor readers need shorter sentences). But we have no integrated model which brings all these factors together into a single algorithm. With regard to the second issue, there have been some studies of different types of aggregation, and how they should be carried out. Harbusch and Kempen describe several syntactic aggregation strategies. In their terminology, John went to the shop and bought an apple is an example of forward conjunction Reduction Much less is known about conceptual aggregation. Di Eugenio et al. show how conceptual aggregation can be done in an intelligent tutoring system, and demonstrate that performing such aggregation makes the system more effective (and that conceptual aggregation make a bigger impact than syntactic aggregation). == Software == Unfortunately there is not much software available for performing aggregation. However the SimpleNLG system does include limited support for basic aggregation. For example, the following code causes SimpleNLG to print out The man is hungry and buys an apple.
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).