Transkribus is a platform for the text recognition, image analysis and structure recognition of historical documents. The platform was created in the context of the two EU projects "tranScriptorium" (2013–2015) and "READ" (Recognition and Enrichment of Archival Documents – 2016–2019). It was developed by the University of Innsbruck. Since July 1, 2019 the platform has been directed and further developed by the READ-COOP, a non-profit cooperative. The platform integrates tools developed by research groups throughout Europe, including the Pattern Recognition and Human Language Technology (PRHLT) group of the Technical University of Valencia and the Computational Intelligence Technology Lab (CITlab) group of University of Rostock. Comparable programs that offer similar functions are eScriptorium and OCR4All.
CLAWS (linguistics)
The Constituent Likelihood Automatic Word-tagging System (CLAWS) is a program that performs part-of-speech tagging. It was developed in the 1980s at Lancaster University by the University Centre for Computer Corpus Research on Language. It has an overall accuracy rate of 96–97% with the latest version (CLAWS4) tagging around 100 million words of the British National Corpus. == History == A Part-Of-Speech Tagger (POS Tagger) is a piece of software that reads text in some language and assigns parts of speech to each word (and other token), such as noun, verb, adjective, etc., although generally computational applications use more fine-grained POS tags like 'noun-plural'. Developed in the early 1980s, CLAWS was built to fill the ever-growing gap created by always-changing POS necessities. Originally created to add part-of-speech tags to the LOB corpus of British English, the CLAWS tagset has since been adapted to other languages as well, including Urdu and Arabic. Since its inception, CLAWS has been hailed for its functionality and adaptability. Still, it is not without flaws, and though it boasts an error-rate of only 1.5% when judged in major categories, CLAWS still remains with c.3.3% ambiguities unresolved. Ambiguity arises in cases such as with the word flies, and whether it should be classified as a noun or a verb. It's these ambiguities that will require the various upgrades and tagsets that CLAWS will endure. == Rules and processing == CLAWS uses a Hidden Markov model to determine the likelihood of sequences of words in anticipating each part-of-speech label. === Sample output === This excerpt from Bram Stoker's Dracula (1897) has been tagged using both the CLAWS C5 and C7 tagsets. This is what a CLAWS output will generally look like, with the most likely part-of-speech tag following each word. == Tagsets == === CLAWS1 tagset === The first tagset developed in CLAWS, CLAWS1 tagset, has 132 word tags. In terms of form and application, C1 tagset is similar to Brown Corpus tags. See Table of tags in C1 tagset here. === CLAWS2 tagset === From 1983 to 1986, updated versions leading to CLAWS2 were part of a larger attempt to deal with aspects such as recognizing sentence breaks, in order to avoid the need for manual pre-processing of a text before the tags were applied, moving instead to optional manual post-editing to adjust the output of the automatic annotation, if needed. The CLAWS2 tagset has 166 word tags. See Table of tags in C2 tagset here. === CLAWS4 tagset === The CLAWS4 was used for the 100-million-word British National Corpus (BNC). A general-purpose grammatical tagger, it is a successor of the CLAWS1 tagger. In tagging the BNC, the many rounds of work that went into CLAWS4 focused on making the CLAWS program independent from the tagsets. For example, the BNC project used two tagset versions: "a main tagset (C5) with 62 tags with which the whole of the corpus has been tagged, and a larger (C7) tagset with 152 tags, which has been used to make a selected 'core' sample corpus of two million words." The latest version of CLAWS4 is offered by UCREL, a research center of Lancaster University. === CLAWS5 tagset === The CLAWS5 tagset, which was used for BNC, has over 60 tags. See Table of tags in C5 tagset here. === CLAWS6 tagset === The CLAWS6 tagset was used for the BNC sampler corpus and the COLT corpus. It has over 160 tags, including 13 determiner subtypes. See Table of tags in C6 tagset here. === CLAWS7 tagset === The standard CLAWS7 tagset is used currently. It is only different in the punctuation tags when compared to the CLAWS6 tagset. See Table of tags in C7 tagset here. === CLAWS8 tagset === CLAWS8 tagset was extended from C7 tagset with further distinctions in the determiner and pronoun categories, as well as 37 new auxiliary tags for forms of be, do, and have. See Table of tags in C8 tagset here
Policy gradient method
Policy gradient methods are a class of reinforcement learning algorithms and a sub-class of policy optimization methods. Unlike value-based methods which learn a value function to derive a policy, policy optimization methods directly learn a policy function π {\displaystyle \pi } that selects actions without consulting a value function. For policy gradient to apply, the policy function π θ {\displaystyle \pi _{\theta }} is parameterized by a differentiable parameter θ {\displaystyle \theta } . == Overview == In policy-based RL, the actor is a parameterized policy function π θ {\displaystyle \pi _{\theta }} , where θ {\displaystyle \theta } are the parameters of the actor. The actor takes as argument the state of the environment s {\displaystyle s} and produces a probability distribution π θ ( ⋅ ∣ s ) {\displaystyle \pi _{\theta }(\cdot \mid s)} . If the action space is discrete, then ∑ a π θ ( a ∣ s ) = 1 {\displaystyle \sum _{a}\pi _{\theta }(a\mid s)=1} . If the action space is continuous, then ∫ a π θ ( a ∣ s ) d a = 1 {\displaystyle \int _{a}\pi _{\theta }(a\mid s)\mathrm {d} a=1} . The goal of policy optimization is to find some θ {\displaystyle \theta } that maximizes the expected episodic reward J ( θ ) {\displaystyle J(\theta )} : J ( θ ) = E π θ [ ∑ t = 0 T γ t R t | S 0 = s 0 ] {\displaystyle J(\theta )=\mathbb {E} _{\pi _{\theta }}\left[\sum _{t=0}^{T}\gamma ^{t}R_{t}{\Big |}S_{0}=s_{0}\right]} where γ {\displaystyle \gamma } is the discount factor, R t {\displaystyle R_{t}} is the reward at step t {\displaystyle t} , s 0 {\displaystyle s_{0}} is the starting state, and T {\displaystyle T} is the time-horizon (which can be infinite). The policy gradient is defined as ∇ θ J ( θ ) {\displaystyle \nabla _{\theta }J(\theta )} . Different policy gradient methods stochastically estimate the policy gradient in different ways. The goal of any policy gradient method is to iteratively maximize J ( θ ) {\displaystyle J(\theta )} by gradient ascent. Since the key part of any policy gradient method is the stochastic estimation of the policy gradient, they are also studied under the title of "Monte Carlo gradient estimation". == REINFORCE == === Policy gradient === The REINFORCE algorithm, introduced by Ronald J. Williams in 1992, was the first policy gradient method. It is based on the identity for the policy gradient ∇ θ J ( θ ) = E π θ [ ∑ t = 0 T ∇ θ ln π θ ( A t ∣ S t ) ∑ t = 0 T ( γ t R t ) | S 0 = s 0 ] {\displaystyle \nabla _{\theta }J(\theta )=\mathbb {E} _{\pi _{\theta }}\left[\sum _{t=0}^{T}\nabla _{\theta }\ln \pi _{\theta }(A_{t}\mid S_{t})\;\sum _{t=0}^{T}(\gamma ^{t}R_{t}){\Big |}S_{0}=s_{0}\right]} which can be improved via the "causality trick" ∇ θ J ( θ ) = E π θ [ ∑ t = 0 T ∇ θ ln π θ ( A t ∣ S t ) ∑ τ = t T ( γ τ R τ ) | S 0 = s 0 ] {\displaystyle \nabla _{\theta }J(\theta )=\mathbb {E} _{\pi _{\theta }}\left[\sum _{t=0}^{T}\nabla _{\theta }\ln \pi _{\theta }(A_{t}\mid S_{t})\sum _{\tau =t}^{T}(\gamma ^{\tau }R_{\tau }){\Big |}S_{0}=s_{0}\right]} Thus, we have an unbiased estimator of the policy gradient: ∇ θ J ( θ ) ≈ 1 N ∑ n = 1 N [ ∑ t = 0 T ∇ θ ln π θ ( A t , n ∣ S t , n ) ∑ τ = t T ( γ τ − t R τ , n ) ] {\displaystyle \nabla _{\theta }J(\theta )\approx {\frac {1}{N}}\sum _{n=1}^{N}\left[\sum _{t=0}^{T}\nabla _{\theta }\ln \pi _{\theta }(A_{t,n}\mid S_{t,n})\sum _{\tau =t}^{T}(\gamma ^{\tau -t}R_{\tau ,n})\right]} where the index n {\displaystyle n} ranges over N {\displaystyle N} rollout trajectories using the policy π θ {\displaystyle \pi _{\theta }} . The score function ∇ θ ln π θ ( A t ∣ S t ) {\displaystyle \nabla _{\theta }\ln \pi _{\theta }(A_{t}\mid S_{t})} can be interpreted as the direction in the parameter space that increases the probability of taking action A t {\displaystyle A_{t}} in state S t {\displaystyle S_{t}} . The policy gradient, then, is a weighted average of all possible directions to increase the probability of taking any action in any state, but weighted by reward signals, so that if taking a certain action in a certain state is associated with high reward, then that direction would be highly reinforced, and vice versa. === Algorithm === The REINFORCE algorithm is a loop: Rollout N {\displaystyle N} trajectories in the environment, using π θ t {\displaystyle \pi _{\theta _{t}}} as the policy function. Compute the policy gradient estimation: g i ← 1 N ∑ n = 1 N [ ∑ t = 0 T ∇ θ t ln π θ ( A t , n ∣ S t , n ) ∑ τ = t T ( γ τ R τ , n ) ] {\displaystyle g_{i}\leftarrow {\frac {1}{N}}\sum _{n=1}^{N}\left[\sum _{t=0}^{T}\nabla _{\theta _{t}}\ln \pi _{\theta }(A_{t,n}\mid S_{t,n})\sum _{\tau =t}^{T}(\gamma ^{\tau }R_{\tau ,n})\right]} Update the policy by gradient ascent: θ i + 1 ← θ i + α i g i {\displaystyle \theta _{i+1}\leftarrow \theta _{i}+\alpha _{i}g_{i}} Here, α i {\displaystyle \alpha _{i}} is the learning rate at update step i {\displaystyle i} . == Variance reduction == REINFORCE is an on-policy algorithm, meaning that the trajectories used for the update must be sampled from the current policy π θ {\displaystyle \pi _{\theta }} . This can lead to high variance in the updates, as the returns R ( τ ) {\displaystyle R(\tau )} can vary significantly between trajectories. Many variants of REINFORCE have been introduced, under the title of variance reduction. === REINFORCE with baseline === A common way for reducing variance is the REINFORCE with baseline algorithm, based on the following identity: ∇ θ J ( θ ) = E π θ [ ∑ t = 0 T ∇ θ ln π θ ( A t | S t ) ( ∑ τ = t T ( γ τ R τ ) − b ( S t ) ) | S 0 = s 0 ] {\displaystyle \nabla _{\theta }J(\theta )=\mathbb {E} _{\pi _{\theta }}\left[\sum _{t=0}^{T}\nabla _{\theta }\ln \pi _{\theta }(A_{t}|S_{t})\left(\sum _{\tau =t}^{T}(\gamma ^{\tau }R_{\tau })-b(S_{t})\right){\Big |}S_{0}=s_{0}\right]} for any function b : States → R {\displaystyle b:{\text{States}}\to \mathbb {R} } . This can be proven by applying the previous lemma. The algorithm uses the modified gradient estimator g i ← 1 N ∑ n = 1 N [ ∑ t = 0 T ∇ θ t ln π θ ( A t , n | S t , n ) ( ∑ τ = t T ( γ τ R τ , n ) − b i ( S t , n ) ) ] {\displaystyle g_{i}\leftarrow {\frac {1}{N}}\sum _{n=1}^{N}\left[\sum _{t=0}^{T}\nabla _{\theta _{t}}\ln \pi _{\theta }(A_{t,n}|S_{t,n})\left(\sum _{\tau =t}^{T}(\gamma ^{\tau }R_{\tau ,n})-b_{i}(S_{t,n})\right)\right]} and the original REINFORCE algorithm is the special case where b i ≡ 0 {\displaystyle b_{i}\equiv 0} . === Actor-critic methods === If b i {\textstyle b_{i}} is chosen well, such that b i ( S t ) ≈ ∑ τ = t T ( γ τ R τ ) = γ t V π θ i ( S t ) {\textstyle b_{i}(S_{t})\approx \sum _{\tau =t}^{T}(\gamma ^{\tau }R_{\tau })=\gamma ^{t}V^{\pi _{\theta _{i}}}(S_{t})} , this could significantly decrease variance in the gradient estimation. That is, the baseline should be as close to the value function V π θ i ( S t ) {\displaystyle V^{\pi _{\theta _{i}}}(S_{t})} as possible, approaching the ideal of: ∇ θ J ( θ ) = E π θ [ ∑ t = 0 T ∇ θ ln π θ ( A t | S t ) ( ∑ τ = t T ( γ τ R τ ) − γ t V π θ ( S t ) ) | S 0 = s 0 ] {\displaystyle \nabla _{\theta }J(\theta )=\mathbb {E} _{\pi _{\theta }}\left[\sum _{t=0}^{T}\nabla _{\theta }\ln \pi _{\theta }(A_{t}|S_{t})\left(\sum _{\tau =t}^{T}(\gamma ^{\tau }R_{\tau })-\gamma ^{t}V^{\pi _{\theta }}(S_{t})\right){\Big |}S_{0}=s_{0}\right]} Note that, as the policy π θ t {\displaystyle \pi _{\theta _{t}}} updates, the value function V π θ i ( S t ) {\displaystyle V^{\pi _{\theta _{i}}}(S_{t})} updates as well, so the baseline should also be updated. One common approach is to train a separate function that estimates the value function, and use that as the baseline. This is one of the actor-critic methods, where the policy function is the actor and the value function is the critic. The Q-function Q π {\displaystyle Q^{\pi }} can also be used as the critic, since ∇ θ J ( θ ) = E π θ [ ∑ 0 ≤ t ≤ T γ t ∇ θ ln π θ ( A t | S t ) ⋅ Q π θ ( S t , A t ) | S 0 = s 0 ] {\displaystyle \nabla _{\theta }J(\theta )=E_{\pi _{\theta }}\left[\sum _{0\leq t\leq T}\gamma ^{t}\nabla _{\theta }\ln \pi _{\theta }(A_{t}|S_{t})\cdot Q^{\pi _{\theta }}(S_{t},A_{t}){\Big |}S_{0}=s_{0}\right]} by a similar argument using the tower law. Subtracting the value function as a baseline, we find that the advantage function A π ( S , A ) = Q π ( S , A ) − V π ( S ) {\displaystyle A^{\pi }(S,A)=Q^{\pi }(S,A)-V^{\pi }(S)} can be used as the critic as well: ∇ θ J ( θ ) = E π θ [ ∑ 0 ≤ t ≤ T γ t ∇ θ ln π θ ( A t | S t ) ⋅ A π θ ( S t , A t ) | S 0 = s 0 ] {\displaystyle \nabla _{\theta }J(\theta )=E_{\pi _{\theta }}\left[\sum _{0\leq t\leq T}\gamma ^{t}\nabla _{\theta }\ln \pi _{\theta }(A_{t}|S_{t})\cdot A^{\pi _{\theta }}(S_{t},A_{t}){\Big |}S_{0}=s_{0}\right]} In summary, there are many unbiased estimators for ∇ θ J θ {\textstyle \nabla _{\theta }J_{\theta }} , all in the form of: ∇ θ J ( θ ) = E π θ [ ∑ 0 ≤ t ≤ T ∇ θ ln π θ ( A t | S t ) ⋅ Ψ t | S 0 = s 0 ] {\displaystyle \nabla _{\theta }J(\theta )=E_{\pi _{\theta }}\left[\su
Artificial development
Artificial development, also known as artificial embryogeny or machine intelligence or computational development, is an area of computer science and engineering concerned with computational models motivated by genotype–phenotype mappings in biological systems. Artificial development is often considered a sub-field of evolutionary computation, although the principles of artificial development have also been used within stand-alone computational models. Within evolutionary computation, the need for artificial development techniques was motivated by the perceived lack of scalability and evolvability of direct solution encodings (Tufte, 2008). Artificial development entails indirect solution encoding. Rather than describing a solution directly, an indirect encoding describes (either explicitly or implicitly) the process by which a solution is constructed. Often, but not always, these indirect encodings are based upon biological principles of development such as morphogen gradients, cell division and cellular differentiation (e.g. Doursat 2008), gene regulatory networks (e.g. Guo et al., 2009), degeneracy (Whitacre et al., 2010), grammatical evolution (de Salabert et al., 2006), or analogous computational processes such as re-writing, iteration, and time. The influences of interaction with the environment, spatiality and physical constraints on differentiated multi-cellular development have been investigated more recently (e.g. Knabe et al. 2008). Artificial development approaches have been applied to a number of computational and design problems, including electronic circuit design (Miller and Banzhaf 2003), robotic controllers (e.g. Taylor 2004), and the design of physical structures (e.g. Hornby 2004).
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
Data remanence
Data remanence is the residual representation of digital data that remains even after attempts have been made to remove or erase the data. This residue may result from data being left intact by a nominal file deletion operation, by reformatting of storage media that does not remove data previously written to the media, or through physical properties of the storage media that allow previously written data to be recovered. Data remanence may make inadvertent disclosure of sensitive information possible should the storage media be released into an uncontrolled environment (e.g., thrown in refuse containers or lost). Various techniques have been developed to counter data remanence. These techniques are classified as clearing, purging/sanitizing, or destruction. Specific methods include overwriting, degaussing, encryption, and media destruction. Effective application of countermeasures can be complicated by several factors, including media that are inaccessible, media that cannot effectively be erased, advanced storage systems that maintain histories of data throughout the data's life cycle, and persistence of data in memory that is typically considered volatile. Several standards exist for the secure removal of data and the elimination of data remanence. == Causes == Many operating systems, file managers, and other software provide a facility where a file is not immediately deleted when the user requests that action. Instead, the file is moved to a holding area (i.e. the "trash"), making it easy for the user to undo a mistake. Similarly, many software products automatically create backup copies of files that are being edited, to allow the user to restore the original version, or to recover from a possible crash (autosave feature). Even when an explicit deleted file retention facility is not provided or when the user does not use it, operating systems do not actually remove the contents of a file when it is deleted unless they are aware that explicit erasure commands are required, like on a solid-state drive. (In such cases, the operating system will issue the Serial ATA TRIM command or the SCSI UNMAP command to let the drive know to no longer maintain the deleted data.) Instead, they simply remove the file's entry from the file system directory because this requires less work and is therefore faster, and the contents of the file—the actual data—remain on the storage medium. The data will remain there until the operating system reuses the space for new data. In some systems, enough filesystem metadata are also left behind to enable easy undeletion by commonly available utility software. Even when undelete has become impossible, the data, until it has been overwritten, can be read by software that reads disk sectors directly. Computer forensics often employs such software. Likewise, reformatting, repartitioning, or reimaging a system is unlikely to write to every area of the disk, though all will cause the disk to appear empty or, in the case of reimaging, empty except for the files present in the image, to most software. Finally, even when the storage media is overwritten, physical properties of the media may permit recovery of the previous contents. In most cases however, this recovery is not possible by just reading from the storage device in the usual way, but requires using laboratory techniques such as disassembling the device and directly accessing/reading from its components. § Complications below gives further explanations for causes of data remanence. == Countermeasures == There are three levels commonly recognized for eliminating remnant data: === Clearing === Clearing is the removal of sensitive data from storage devices in such a way that there is assurance that the data may not be reconstructed using normal system functions or software file/data recovery utilities. The data may still be recoverable, but not without special laboratory techniques. Clearing is typically an administrative protection against accidental disclosure within an organization. For example, before a hard drive is re-used within an organization, its contents may be cleared to prevent their accidental disclosure to the next user. === Purging === Purging or sanitizing is the physical rewrite of sensitive data from a system or storage device done with the specific intent of rendering the data unrecoverable at a later time. Purging, proportional to the sensitivity of the data, is generally done before releasing media beyond control, such as before discarding old media, or moving media to a computer with different security requirements. === Destruction === The storage media is made unusable for conventional equipment. Effectiveness of destroying the media varies by medium and method. Depending on recording density of the media, and/or the destruction technique, this may leave data recoverable by laboratory methods. Conversely, destruction using appropriate techniques is the most secure method of preventing retrieval. == Specific methods == === Overwriting === A common method used to counter data remanence is to overwrite the storage media with new data. This is often called wiping or shredding a disk or file, by analogy to common methods of destroying print media, although the mechanism bears no similarity to these. Because such a method can often be implemented in software alone, and may be able to selectively target only part of the media, it is a popular, low-cost option for some applications. Overwriting is generally an acceptable method of clearing, as long as the media is writable and not damaged. The simplest overwrite technique writes the same data everywhere—often just a pattern of all zeros. At a minimum, this will prevent the data from being retrieved simply by reading from the media again using standard system functions. The UEFI in modern machines may offer an ATA class disk erase function as well. The ATA-6 standard governs secure erases specifications. Bitlocker is whole disk encryption and illegible without the key. Writing a fresh GPT allows a new file system to be established. Blocks will set empty but LBA read is illegible. New data will be unaffected and work fine. In an attempt to counter more advanced data recovery techniques, specific overwrite patterns and multiple passes have often been prescribed. These may be generic patterns intended to eradicate any trace signatures; an example is the seven-pass pattern 0xF6, 0x00, 0xFF,
Nonlinear dimensionality reduction
Nonlinear dimensionality reduction (NLDR), also known as manifold learning, is any of various related techniques that aim to project high-dimensional data, potentially existing across non-linear manifolds which cannot be adequately captured by linear decomposition methods, onto lower-dimensional latent manifolds, with the goal of either visualizing the data in the low-dimensional space, or learning the mapping (either from the high-dimensional space to the low-dimensional embedding or vice versa) itself. The techniques described below can be understood as generalizations of linear decomposition methods used for dimensionality reduction, such as singular value decomposition and principal component analysis. == Applications of NLDR == High dimensional data can be hard for machines to work with, requiring significant time and space for analysis. It also presents a challenge for humans, since it's hard to visualize or understand data in more than three dimensions. Reducing the dimensionality of a data set, while keeping its essential features relatively intact, can make algorithms more efficient and allow analysts to visualize trends and patterns. The reduced-dimensional representations of data are often referred to as "intrinsic variables". This description implies that these are the values from which the data was produced. For example, consider a dataset that contains images of a letter 'A', which has been scaled and rotated by varying amounts. Each image has 32×32 pixels. Each image can be represented as a vector of 1024 pixel values. Each row is a sample on a two-dimensional manifold in 1024-dimensional space (a Hamming space). The intrinsic dimensionality is two, because two variables (rotation and scale) were varied in order to produce the data. Information about the shape or look of a letter 'A' is not part of the intrinsic variables because it is the same in every instance. Nonlinear dimensionality reduction will discard the correlated information (the letter 'A') and recover only the varying information (rotation and scale). By comparison, if principal component analysis, which is a linear dimensionality reduction algorithm, is used to reduce this same dataset into two dimensions, the resulting values are not so well organized. This demonstrates that the high-dimensional vectors (each representing a letter 'A') that sample this manifold vary in a non-linear manner. It should be apparent, therefore, that NLDR has several applications in the field of computer-vision. For example, consider a robot that uses a camera to navigate in a closed static environment. The images obtained by that camera can be considered to be samples on a manifold in high-dimensional space, and the intrinsic variables of that manifold will represent the robot's position and orientation. Invariant manifolds are of general interest for model order reduction in dynamical systems. In particular, if there is an attracting invariant manifold in the phase space, nearby trajectories will converge onto it and stay on it indefinitely, rendering it a candidate for dimensionality reduction of the dynamical system. While such manifolds are not guaranteed to exist in general, the theory of spectral submanifolds (SSM) gives conditions for the existence of unique attracting invariant objects in a broad class of dynamical systems. Active research in NLDR seeks to unfold the observation manifolds associated with dynamical systems to develop modeling techniques. Some of the more prominent nonlinear dimensionality reduction techniques are listed below. == Important concepts == === Sammon's mapping === Sammon's mapping is one of the first and most popular NLDR techniques. === Self-organizing map === The self-organizing map (SOM, also called Kohonen map) and its probabilistic variant generative topographic mapping (GTM) use a point representation in the embedded space to form a latent variable model based on a non-linear mapping from the embedded space to the high-dimensional space. These techniques are related to work on density networks, which also are based around the same probabilistic model. === Kernel principal component analysis === Perhaps the most widely used algorithm for dimensional reduction is kernel PCA. PCA begins by computing the covariance matrix of the m × n {\displaystyle m\times n} matrix X {\displaystyle \mathbf {X} } C = 1 m ∑ i = 1 m x i x i T . {\displaystyle C={\frac {1}{m}}\sum _{i=1}^{m}{\mathbf {x} _{i}\mathbf {x} _{i}^{\mathsf {T}}}.} It then projects the data onto the first k eigenvectors of that matrix. By comparison, KPCA begins by computing the covariance matrix of the data after being transformed into a higher-dimensional space, C = 1 m ∑ i = 1 m Φ ( x i ) Φ ( x i ) T . {\displaystyle C={\frac {1}{m}}\sum _{i=1}^{m}{\Phi (\mathbf {x} _{i})\Phi (\mathbf {x} _{i})^{\mathsf {T}}}.} It then projects the transformed data onto the first k eigenvectors of that matrix, just like PCA. It uses the kernel trick to factor away much of the computation, such that the entire process can be performed without actually computing Φ ( x ) {\displaystyle \Phi (\mathbf {x} )} . Of course Φ {\displaystyle \Phi } must be chosen such that it has a known corresponding kernel. Unfortunately, it is not trivial to find a good kernel for a given problem, so KPCA does not yield good results with some problems when using standard kernels. For example, it is known to perform poorly with these kernels on the Swiss roll manifold. However, one can view certain other methods that perform well in such settings (e.g., Laplacian Eigenmaps, LLE) as special cases of kernel PCA by constructing a data-dependent kernel matrix. KPCA has an internal model, so it can be used to map points onto its embedding that were not available at training time. === Principal curves and manifolds === Principal curves and manifolds give the natural geometric framework for nonlinear dimensionality reduction and extend the geometric interpretation of PCA by explicitly constructing an embedded manifold, and by encoding using standard geometric projection onto the manifold. This approach was originally proposed by Trevor Hastie in his 1984 thesis, which he formally introduced in 1989. This idea has been explored further by many authors. How to define the "simplicity" of the manifold is problem-dependent, however, it is commonly measured by the intrinsic dimensionality and/or the smoothness of the manifold. Usually, the principal manifold is defined as a solution to an optimization problem. The objective function includes a quality of data approximation and some penalty terms for the bending of the manifold. The popular initial approximations are generated by linear PCA and Kohonen's SOM. === Laplacian eigenmaps === Laplacian eigenmaps uses spectral techniques to perform dimensionality reduction. This technique relies on the basic assumption that the data lies in a low-dimensional manifold in a high-dimensional space. This algorithm cannot embed out-of-sample points, but techniques based on Reproducing kernel Hilbert space regularization exist for adding this capability. Such techniques can be applied to other nonlinear dimensionality reduction algorithms as well. Traditional techniques like principal component analysis do not consider the intrinsic geometry of the data. Laplacian eigenmaps builds a graph from neighborhood information of the data set. Each data point serves as a node on the graph and connectivity between nodes is governed by the proximity of neighboring points (using e.g. the k-nearest neighbor algorithm). The graph thus generated can be considered as a discrete approximation of the low-dimensional manifold in the high-dimensional space. Minimization of a cost function based on the graph ensures that points close to each other on the manifold are mapped close to each other in the low-dimensional space, preserving local distances. The eigenfunctions of the Laplace–Beltrami operator on the manifold serve as the embedding dimensions, since under mild conditions this operator has a countable spectrum that is a basis for square integrable functions on the manifold (compare to Fourier series on the unit circle manifold). Attempts to place Laplacian eigenmaps on solid theoretical ground have met with some success, as under certain nonrestrictive assumptions, the graph Laplacian matrix has been shown to converge to the Laplace–Beltrami operator as the number of points goes to infinity. === Isomap === Isomap is a combination of the Floyd–Warshall algorithm with classic Multidimensional Scaling (MDS). Classic MDS takes a matrix of pair-wise distances between all points and computes a position for each point. Isomap assumes that the pair-wise distances are only known between neighboring points, and uses the Floyd–Warshall algorithm to compute the pair-wise distances between all other points. This effectively estimates the full matrix of pair-wise geodesic distances between all of the points. Isomap th