In computing, external memory algorithms or out-of-core algorithms are algorithms that are designed to process data that are too large to fit into a computer's main memory at once. Such algorithms must be optimized to efficiently fetch and access data stored in slow bulk memory (auxiliary memory) such as hard drives or tape drives, or when memory is on a computer network. External memory algorithms are analyzed in the external memory model. == Model == External memory algorithms are analyzed in an idealized model of computation called the external memory model (or I/O model, or disk access model). The external memory model is an abstract machine similar to the RAM machine model, but with a cache in addition to main memory. The model captures the fact that read and write operations are much faster in a cache than in main memory, and that reading long contiguous blocks is faster than reading randomly using a disk read-and-write head. The running time of an algorithm in the external memory model is defined by the number of reads and writes to memory required. The model was introduced by Alok Aggarwal and Jeffrey Vitter in 1988. The external memory model is related to the cache-oblivious model, but algorithms in the external memory model may know both the block size and the cache size. For this reason, the model is sometimes referred to as the cache-aware model. The model consists of a processor with an internal memory or cache of size M, connected to an unbounded external memory. Both the internal and external memory are divided into blocks of size B. One input/output or memory transfer operation consists of moving a block of B contiguous elements from external to internal memory, and the running time of an algorithm is determined by the number of these input/output operations. == Algorithms == Algorithms in the external memory model take advantage of the fact that retrieving one object from external memory retrieves an entire block of size B. This property is sometimes referred to as locality. Searching for an element among N objects is possible in the external memory model using a B-tree with branching factor B. Using a B-tree, searching, insertion, and deletion can be achieved in O ( log B N ) {\displaystyle O(\log _{B}N)} time (in Big O notation). Information theoretically, this is the minimum running time possible for these operations, so using a B-tree is asymptotically optimal. External sorting is sorting in an external memory setting. External sorting can be done via distribution sort, which is similar to quicksort, or via a M B {\displaystyle {\tfrac {M}{B}}} -way merge sort. Both variants achieve the asymptotically optimal runtime of O ( N B log M B N B ) {\displaystyle O\left({\frac {N}{B}}\log _{\frac {M}{B}}{\frac {N}{B}}\right)} to sort N objects. This bound also applies to the fast Fourier transform in the external memory model. The permutation problem is to rearrange N elements into a specific permutation. This can either be done either by sorting, which requires the above sorting runtime, or inserting each element in order and ignoring the benefit of locality. Thus, permutation can be done in O ( min ( N , N B log M B N B ) ) {\displaystyle O\left(\min \left(N,{\frac {N}{B}}\log _{\frac {M}{B}}{\frac {N}{B}}\right)\right)} time. == Applications == The external memory model captures the memory hierarchy, which is not modeled in other common models used in analyzing data structures, such as the random-access machine, and is useful for proving lower bounds for data structures. The model is also useful for analyzing algorithms that work on datasets too big to fit in internal memory. A typical example is geographic information systems, especially digital elevation models, where the full data set easily exceeds several gigabytes or even terabytes of data. This methodology extends beyond general purpose CPUs and also includes GPU computing as well as classical digital signal processing. In general-purpose computing on graphics processing units (GPGPU), powerful graphics cards (GPUs) with little memory (compared with the more familiar system memory, which is most often referred to simply as RAM) are utilized with relatively slow CPU-to-GPU memory transfer (when compared with computation bandwidth). == History == An early use of the term "out-of-core" as an adjective is in 1962 in reference to devices that are other than the core memory of an IBM 360. An early use of the term "out-of-core" with respect to algorithms appears in 1971.
Cross-entropy method
The cross-entropy (CE) method is a Monte Carlo method for importance sampling and optimization. It is applicable to both combinatorial and continuous problems, with either a static or noisy objective. The method approximates the optimal importance sampling estimator by repeating two phases: Draw a sample from a probability distribution. Minimize the cross-entropy between this distribution and a target distribution to produce a better sample in the next iteration. Reuven Rubinstein developed the method in the context of rare-event simulation, where tiny probabilities must be estimated, for example in network reliability analysis, queueing models, or performance analysis of telecommunication systems. The method has also been applied to the traveling salesman, quadratic assignment, DNA sequence alignment, max-cut and buffer allocation problems. == Estimation via importance sampling == Consider the general problem of estimating the quantity ℓ = E u [ H ( X ) ] = ∫ H ( x ) f ( x ; u ) d x {\displaystyle \ell =\mathbb {E} _{\mathbf {u} }[H(\mathbf {X} )]=\int H(\mathbf {x} )\,f(\mathbf {x} ;\mathbf {u} )\,{\textrm {d}}\mathbf {x} } , where H {\displaystyle H} is some performance function and f ( x ; u ) {\displaystyle f(\mathbf {x} ;\mathbf {u} )} is a member of some parametric family of distributions. Using importance sampling this quantity can be estimated as ℓ ^ = 1 N ∑ i = 1 N H ( X i ) f ( X i ; u ) g ( X i ) {\displaystyle {\hat {\ell }}={\frac {1}{N}}\sum _{i=1}^{N}H(\mathbf {X} _{i}){\frac {f(\mathbf {X} _{i};\mathbf {u} )}{g(\mathbf {X} _{i})}}} , where X 1 , … , X N {\displaystyle \mathbf {X} _{1},\dots ,\mathbf {X} _{N}} is a random sample from g {\displaystyle g\,} . For positive H {\displaystyle H} , the theoretically optimal importance sampling density (PDF) is given by g ∗ ( x ) = H ( x ) f ( x ; u ) / ℓ {\displaystyle g^{}(\mathbf {x} )=H(\mathbf {x} )f(\mathbf {x} ;\mathbf {u} )/\ell } . This, however, depends on the unknown ℓ {\displaystyle \ell } . The CE method aims to approximate the optimal PDF by adaptively selecting members of the parametric family that are closest (in the Kullback–Leibler sense) to the optimal PDF g ∗ {\displaystyle g^{}} . == Generic CE algorithm == Choose initial parameter vector v ( 0 ) {\displaystyle \mathbf {v} ^{(0)}} ; set t = 1. Generate a random sample X 1 , … , X N {\displaystyle \mathbf {X} _{1},\dots ,\mathbf {X} _{N}} from f ( ⋅ ; v ( t − 1 ) ) {\displaystyle f(\cdot ;\mathbf {v} ^{(t-1)})} Solve for v ( t ) {\displaystyle \mathbf {v} ^{(t)}} , where v ( t ) = argmax v 1 N ∑ i = 1 N H ( X i ) f ( X i ; u ) f ( X i ; v ( t − 1 ) ) log f ( X i ; v ) {\displaystyle \mathbf {v} ^{(t)}=\mathop {\textrm {argmax}} _{\mathbf {v} }{\frac {1}{N}}\sum _{i=1}^{N}H(\mathbf {X} _{i}){\frac {f(\mathbf {X} _{i};\mathbf {u} )}{f(\mathbf {X} _{i};\mathbf {v} ^{(t-1)})}}\log f(\mathbf {X} _{i};\mathbf {v} )} If convergence is reached then stop; otherwise, increase t by 1 and reiterate from step 2. In several cases, the solution to step 3 can be found analytically. Situations in which this occurs are When f {\displaystyle f\,} belongs to the natural exponential family When f {\displaystyle f\,} is discrete with finite support When H ( X ) = I { x ∈ A } {\displaystyle H(\mathbf {X} )=\mathrm {I} _{\{\mathbf {x} \in A\}}} and f ( X i ; u ) = f ( X i ; v ( t − 1 ) ) {\displaystyle f(\mathbf {X} _{i};\mathbf {u} )=f(\mathbf {X} _{i};\mathbf {v} ^{(t-1)})} , then v ( t ) {\displaystyle \mathbf {v} ^{(t)}} corresponds to the maximum likelihood estimator based on those X k ∈ A {\displaystyle \mathbf {X} _{k}\in A} . == Continuous optimization—example == The same CE algorithm can be used for optimization, rather than estimation. Suppose the problem is to maximize some function S {\displaystyle S} , for example, S ( x ) = e − ( x − 2 ) 2 + 0.8 e − ( x + 2 ) 2 {\displaystyle S(x)={\textrm {e}}^{-(x-2)^{2}}+0.8\,{\textrm {e}}^{-(x+2)^{2}}} . To apply CE, one considers first the associated stochastic problem of estimating P θ ( S ( X ) ≥ γ ) {\displaystyle \mathbb {P} _{\boldsymbol {\theta }}(S(X)\geq \gamma )} for a given level γ {\displaystyle \gamma \,} , and parametric family { f ( ⋅ ; θ ) } {\displaystyle \left\{f(\cdot ;{\boldsymbol {\theta }})\right\}} , for example the 1-dimensional Gaussian distribution, parameterized by its mean μ t {\displaystyle \mu _{t}\,} and variance σ t 2 {\displaystyle \sigma _{t}^{2}} (so θ = ( μ , σ 2 ) {\displaystyle {\boldsymbol {\theta }}=(\mu ,\sigma ^{2})} here). Hence, for a given γ {\displaystyle \gamma \,} , the goal is to find θ {\displaystyle {\boldsymbol {\theta }}} so that D K L ( I { S ( x ) ≥ γ } ‖ f θ ) {\displaystyle D_{\mathrm {KL} }({\textrm {I}}_{\{S(x)\geq \gamma \}}\|f_{\boldsymbol {\theta }})} is minimized. This is done by solving the sample version (stochastic counterpart) of the KL divergence minimization problem, as in step 3 above. It turns out that parameters that minimize the stochastic counterpart for this choice of target distribution and parametric family are the sample mean and sample variance corresponding to the elite samples, which are those samples that have objective function value ≥ γ {\displaystyle \geq \gamma } . The worst of the elite samples is then used as the level parameter for the next iteration. This yields the following randomized algorithm that happens to coincide with the so-called Estimation of Multivariate Normal Algorithm (EMNA), an estimation of distribution algorithm. === Pseudocode === // Initialize parameters μ := −6 σ2 := 100 t := 0 maxits := 100 N := 100 Ne := 10 // While maxits not exceeded and not converged while t < maxits and σ2 > ε do // Obtain N samples from current sampling distribution X := SampleGaussian(μ, σ2, N) // Evaluate objective function at sampled points S := exp(−(X − 2) ^ 2) + 0.8 exp(−(X + 2) ^ 2) // Sort X by objective function values in descending order X := sort(X, S) // Update parameters of sampling distribution via elite samples μ := mean(X(1:Ne)) σ2 := var(X(1:Ne)) t := t + 1 // Return mean of final sampling distribution as solution return μ == Related methods == Simulated annealing Genetic algorithms Harmony search Estimation of distribution algorithm Tabu search Natural Evolution Strategy Ant colony optimization algorithms
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Deepti Gurdasani
Deepti Gurdasani is a British-Indian clinical epidemiologist and statistical geneticist who is a senior lecturer in machine learning at the Queen Mary University of London. Her research considers the genetic diversity of African Populations. Throughout the COVID-19 pandemic, Gurdasani has provided the public with her analysis of the evolving situation mainly on the Twitter platform. == Early life and education == Gurdasani was an undergraduate and medical student at the Christian Medical College Vellore at Tamil Nadu Dr. M.G.R. Medical University. After earning her medical degree and qualifying in internal medicine, she moved to the United Kingdom, where she worked toward a research doctorate in genetic epidemiology at Wolfson College, Cambridge. Her doctoral research involved the design of strategies to understand complex diseases in diverse populations. == Research and career == In 2013, Gurdasani joined the Wellcome Sanger Institute as a postdoctoral fellow, where she worked on the genomic diversity of African populations and how this diversity impacts susceptibility to disease. She makes use of dense genotypes and whole genome sequences to better understand how population movements determined genetic structure. In particular, Gurdasani develops machine learning algorithms to large-scale clinical data sets. At the Sanger Gurdasani co-led the African Genome Variation Project and the Uganda Resource Project. Gurdasani moved to Queen Mary University of London in 2019, where she created deep learning approaches for clinical prediction and the identification of novel, genome-based drug targets. During the COVID-19 pandemic Gurdasani has provided public commentary on the pandemic, making use of both Twitter and print media to share information on the evolving situation. She has researched the incidence of long covid in the UK. In 2021 Gurdasani started to write for The Guardian. == Selected publications == Deepti Gurdasani; Tommy Carstensen; Fasil Tekola-Ayele; et al. (3 December 2014). "The African Genome Variation Project shapes medical genetics in Africa". Nature. 517 (7534): 327–332. doi:10.1038/NATURE13997. ISSN 1476-4687. PMC 4297536. PMID 25470054. Wikidata Q34979569. Nisreen A Alwan; Rochelle Ann Burgess; Simon Ashworth; et al. (15 October 2020). "Scientific consensus on the COVID-19 pandemic: we need to act now". The Lancet. doi:10.1016/S0140-6736(20)32153-X. ISSN 0140-6736. PMC 7557300. PMID 33069277. Wikidata Q100697134. Deepti Gurdasani; Inês Barroso; Eleftheria Zeggini; Manjinder S Sandhu (24 June 2019). "Genomics of disease risk in globally diverse populations". Nature Reviews Genetics. 20 (9): 520–535. doi:10.1038/S41576-019-0144-0. ISSN 1471-0056. PMID 31235872. Wikidata Q93000887. (erratum)
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Cross-entropy method
The cross-entropy (CE) method is a Monte Carlo method for importance sampling and optimization. It is applicable to both combinatorial and continuous problems, with either a static or noisy objective. The method approximates the optimal importance sampling estimator by repeating two phases: Draw a sample from a probability distribution. Minimize the cross-entropy between this distribution and a target distribution to produce a better sample in the next iteration. Reuven Rubinstein developed the method in the context of rare-event simulation, where tiny probabilities must be estimated, for example in network reliability analysis, queueing models, or performance analysis of telecommunication systems. The method has also been applied to the traveling salesman, quadratic assignment, DNA sequence alignment, max-cut and buffer allocation problems. == Estimation via importance sampling == Consider the general problem of estimating the quantity ℓ = E u [ H ( X ) ] = ∫ H ( x ) f ( x ; u ) d x {\displaystyle \ell =\mathbb {E} _{\mathbf {u} }[H(\mathbf {X} )]=\int H(\mathbf {x} )\,f(\mathbf {x} ;\mathbf {u} )\,{\textrm {d}}\mathbf {x} } , where H {\displaystyle H} is some performance function and f ( x ; u ) {\displaystyle f(\mathbf {x} ;\mathbf {u} )} is a member of some parametric family of distributions. Using importance sampling this quantity can be estimated as ℓ ^ = 1 N ∑ i = 1 N H ( X i ) f ( X i ; u ) g ( X i ) {\displaystyle {\hat {\ell }}={\frac {1}{N}}\sum _{i=1}^{N}H(\mathbf {X} _{i}){\frac {f(\mathbf {X} _{i};\mathbf {u} )}{g(\mathbf {X} _{i})}}} , where X 1 , … , X N {\displaystyle \mathbf {X} _{1},\dots ,\mathbf {X} _{N}} is a random sample from g {\displaystyle g\,} . For positive H {\displaystyle H} , the theoretically optimal importance sampling density (PDF) is given by g ∗ ( x ) = H ( x ) f ( x ; u ) / ℓ {\displaystyle g^{}(\mathbf {x} )=H(\mathbf {x} )f(\mathbf {x} ;\mathbf {u} )/\ell } . This, however, depends on the unknown ℓ {\displaystyle \ell } . The CE method aims to approximate the optimal PDF by adaptively selecting members of the parametric family that are closest (in the Kullback–Leibler sense) to the optimal PDF g ∗ {\displaystyle g^{}} . == Generic CE algorithm == Choose initial parameter vector v ( 0 ) {\displaystyle \mathbf {v} ^{(0)}} ; set t = 1. Generate a random sample X 1 , … , X N {\displaystyle \mathbf {X} _{1},\dots ,\mathbf {X} _{N}} from f ( ⋅ ; v ( t − 1 ) ) {\displaystyle f(\cdot ;\mathbf {v} ^{(t-1)})} Solve for v ( t ) {\displaystyle \mathbf {v} ^{(t)}} , where v ( t ) = argmax v 1 N ∑ i = 1 N H ( X i ) f ( X i ; u ) f ( X i ; v ( t − 1 ) ) log f ( X i ; v ) {\displaystyle \mathbf {v} ^{(t)}=\mathop {\textrm {argmax}} _{\mathbf {v} }{\frac {1}{N}}\sum _{i=1}^{N}H(\mathbf {X} _{i}){\frac {f(\mathbf {X} _{i};\mathbf {u} )}{f(\mathbf {X} _{i};\mathbf {v} ^{(t-1)})}}\log f(\mathbf {X} _{i};\mathbf {v} )} If convergence is reached then stop; otherwise, increase t by 1 and reiterate from step 2. In several cases, the solution to step 3 can be found analytically. Situations in which this occurs are When f {\displaystyle f\,} belongs to the natural exponential family When f {\displaystyle f\,} is discrete with finite support When H ( X ) = I { x ∈ A } {\displaystyle H(\mathbf {X} )=\mathrm {I} _{\{\mathbf {x} \in A\}}} and f ( X i ; u ) = f ( X i ; v ( t − 1 ) ) {\displaystyle f(\mathbf {X} _{i};\mathbf {u} )=f(\mathbf {X} _{i};\mathbf {v} ^{(t-1)})} , then v ( t ) {\displaystyle \mathbf {v} ^{(t)}} corresponds to the maximum likelihood estimator based on those X k ∈ A {\displaystyle \mathbf {X} _{k}\in A} . == Continuous optimization—example == The same CE algorithm can be used for optimization, rather than estimation. Suppose the problem is to maximize some function S {\displaystyle S} , for example, S ( x ) = e − ( x − 2 ) 2 + 0.8 e − ( x + 2 ) 2 {\displaystyle S(x)={\textrm {e}}^{-(x-2)^{2}}+0.8\,{\textrm {e}}^{-(x+2)^{2}}} . To apply CE, one considers first the associated stochastic problem of estimating P θ ( S ( X ) ≥ γ ) {\displaystyle \mathbb {P} _{\boldsymbol {\theta }}(S(X)\geq \gamma )} for a given level γ {\displaystyle \gamma \,} , and parametric family { f ( ⋅ ; θ ) } {\displaystyle \left\{f(\cdot ;{\boldsymbol {\theta }})\right\}} , for example the 1-dimensional Gaussian distribution, parameterized by its mean μ t {\displaystyle \mu _{t}\,} and variance σ t 2 {\displaystyle \sigma _{t}^{2}} (so θ = ( μ , σ 2 ) {\displaystyle {\boldsymbol {\theta }}=(\mu ,\sigma ^{2})} here). Hence, for a given γ {\displaystyle \gamma \,} , the goal is to find θ {\displaystyle {\boldsymbol {\theta }}} so that D K L ( I { S ( x ) ≥ γ } ‖ f θ ) {\displaystyle D_{\mathrm {KL} }({\textrm {I}}_{\{S(x)\geq \gamma \}}\|f_{\boldsymbol {\theta }})} is minimized. This is done by solving the sample version (stochastic counterpart) of the KL divergence minimization problem, as in step 3 above. It turns out that parameters that minimize the stochastic counterpart for this choice of target distribution and parametric family are the sample mean and sample variance corresponding to the elite samples, which are those samples that have objective function value ≥ γ {\displaystyle \geq \gamma } . The worst of the elite samples is then used as the level parameter for the next iteration. This yields the following randomized algorithm that happens to coincide with the so-called Estimation of Multivariate Normal Algorithm (EMNA), an estimation of distribution algorithm. === Pseudocode === // Initialize parameters μ := −6 σ2 := 100 t := 0 maxits := 100 N := 100 Ne := 10 // While maxits not exceeded and not converged while t < maxits and σ2 > ε do // Obtain N samples from current sampling distribution X := SampleGaussian(μ, σ2, N) // Evaluate objective function at sampled points S := exp(−(X − 2) ^ 2) + 0.8 exp(−(X + 2) ^ 2) // Sort X by objective function values in descending order X := sort(X, S) // Update parameters of sampling distribution via elite samples μ := mean(X(1:Ne)) σ2 := var(X(1:Ne)) t := t + 1 // Return mean of final sampling distribution as solution return μ == Related methods == Simulated annealing Genetic algorithms Harmony search Estimation of distribution algorithm Tabu search Natural Evolution Strategy Ant colony optimization algorithms
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