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  • Learning to rank

    Learning to rank

    Learning to rank (LTR) or machine-learned ranking (MLR) is the application of machine learning, often supervised, semi-supervised or reinforcement learning, in the construction of ranking models for information retrieval and recommender systems. Training data may, for example, consist of lists of items with some partial order specified between items in each list. This order is typically induced by giving a numerical or ordinal score or a binary judgment (e.g. "relevant" or "not relevant") for each item. The goal of constructing the ranking model is to rank new, unseen lists in a similar way to rankings in the training data. == Applications == === In information retrieval === Ranking is a central part of many information retrieval problems, such as document retrieval, collaborative filtering, sentiment analysis, and online advertising. A possible architecture of a machine-learned search engine is shown in the accompanying figure. Training data consists of queries and documents matching them together with the relevance degree of each match. It may be prepared manually by human assessors (or raters, as Google calls them), who check results for some queries and determine relevance of each result. It is not feasible to check the relevance of all documents, and so typically a technique called pooling is used — only the top few documents, retrieved by some existing ranking models are checked. This technique may introduce selection bias. Alternatively, training data may be derived automatically by analyzing clickthrough logs (i.e. search results which got clicks from users), query chains, or such search engines' features as Google's (since-replaced) SearchWiki. Clickthrough logs can be biased by the tendency of users to click on the top search results on the assumption that they are already well-ranked. Training data is used by a learning algorithm to produce a ranking model which computes the relevance of documents for actual queries. Typically, users expect a search query to complete in a short time (such as a few hundred milliseconds for web search), which makes it impossible to evaluate a complex ranking model on each document in the corpus, and so a two-phase scheme is used. First, a small number of potentially relevant documents are identified using simpler retrieval models which permit fast query evaluation, such as the vector space model, Boolean model, weighted AND, or BM25. This phase is called top- k {\displaystyle k} document retrieval and many heuristics were proposed in the literature to accelerate it, such as using a document's static quality score and tiered indexes. In the second phase, a more accurate but computationally expensive machine-learned model is used to re-rank these documents. === In other areas === Learning to rank algorithms have been applied in areas other than information retrieval: In machine translation for ranking a set of hypothesized translations; In computational biology for ranking candidate 3-D structures in protein structure prediction problems; In recommender systems for identifying a ranked list of related news articles to recommend to a user after he or she has read a current news article. == Feature vectors == For the convenience of MLR algorithms, query-document pairs are usually represented by numerical vectors, which are called feature vectors. Such an approach is sometimes called bag of features and is analogous to the bag of words model and vector space model used in information retrieval for representation of documents. Components of such vectors are called features, factors or ranking signals. They may be divided into three groups (features from document retrieval are shown as examples): Query-independent or static features — those features, which depend only on the document, but not on the query. For example, PageRank or document's length. Such features can be precomputed in off-line mode during indexing. They may be used to compute document's static quality score (or static rank), which is often used to speed up search query evaluation. Query-dependent or dynamic features — those features, which depend both on the contents of the document and the query, such as TF-IDF score or other non-machine-learned ranking functions. Query-level features or query features, which depend only on the query. For example, the number of words in a query. Some examples of features, which were used in the well-known LETOR dataset: TF, TF-IDF, BM25, and language modeling scores of document's zones (title, body, anchors text, URL) for a given query; Lengths and IDF sums of document's zones; Document's PageRank, HITS ranks and their variants. Selecting and designing good features is an important area in machine learning, which is called feature engineering. == Evaluation measures == There are several measures (metrics) which are commonly used to judge how well an algorithm is doing on training data and to compare the performance of different MLR algorithms. Often a learning-to-rank problem is reformulated as an optimization problem with respect to one of these metrics. Examples of ranking quality measures: Mean average precision (MAP); DCG and NDCG; Precision@n, NDCG@n, where "@n" denotes that the metrics are evaluated only on top n documents; Mean reciprocal rank; Kendall's tau; Spearman's rho. DCG and its normalized variant NDCG are usually preferred in academic research when multiple levels of relevance are used. Other metrics such as MAP, MRR and precision, are defined only for binary judgments. Recently, there have been proposed several new evaluation metrics which claim to model user's satisfaction with search results better than the DCG metric: Expected reciprocal rank (ERR); Yandex's pfound. Both of these metrics are based on the assumption that the user is more likely to stop looking at search results after examining a more relevant document, than after a less relevant document. == Approaches == Learning to Rank approaches are often categorized using one of three approaches: pointwise (where individual documents are ranked), pairwise (where pairs of documents are ranked into a relative order), and listwise (where an entire list of documents are ordered). Tie-Yan Liu of Microsoft Research Asia has analyzed existing algorithms for learning to rank problems in his book Learning to Rank for Information Retrieval. He categorized them into three groups by their input spaces, output spaces, hypothesis spaces (the core function of the model) and loss functions: the pointwise, pairwise, and listwise approach. In practice, listwise approaches often outperform pairwise approaches and pointwise approaches. This statement was further supported by a large scale experiment on the performance of different learning-to-rank methods on a large collection of benchmark data sets. In this section, without further notice, x {\displaystyle x} denotes an object to be evaluated, for example, a document or an image, f ( x ) {\displaystyle f(x)} denotes a single-value hypothesis, h ( ⋅ ) {\displaystyle h(\cdot )} denotes a bi-variate or multi-variate function and L ( ⋅ ) {\displaystyle L(\cdot )} denotes the loss function. === Pointwise approach === In this case, it is assumed that each query-document pair in the training data has a numerical or ordinal score. Then the learning-to-rank problem can be approximated by a regression problem — given a single query-document pair, predict its score. Formally speaking, the pointwise approach aims at learning a function f ( x ) {\displaystyle f(x)} predicting the real-value or ordinal score of a document x {\displaystyle x} using the loss function L ( f ; x j , y j ) {\displaystyle L(f;x_{j},y_{j})} . A number of existing supervised machine learning algorithms can be readily used for this purpose. Ordinal regression and classification algorithms can also be used in pointwise approach when they are used to predict the score of a single query-document pair, and it takes a small, finite number of values. === Pairwise approach === In this case, the learning-to-rank problem is approximated by a classification problem — learning a binary classifier h ( x u , x v ) {\displaystyle h(x_{u},x_{v})} that can tell which document is better in a given pair of documents. The classifier shall take two documents as its input and the goal is to minimize a loss function L ( h ; x u , x v , y u , v ) {\displaystyle L(h;x_{u},x_{v},y_{u,v})} . The loss function typically reflects the number and magnitude of inversions in the induced ranking. In many cases, the binary classifier h ( x u , x v ) {\displaystyle h(x_{u},x_{v})} is implemented with a scoring function f ( x ) {\displaystyle f(x)} . As an example, RankNet adapts a probability model and defines h ( x u , x v ) {\displaystyle h(x_{u},x_{v})} as the estimated probability of the document x u {\displaystyle x_{u}} has higher quality than x v {\displaystyle x_{v}} : P u , v ( f ) = CDF ( f ( x u ) − f ( x v ) ) , {\displaystyle P_{u,v}(f)={\text{CDF}

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  • Zassenhaus algorithm

    Zassenhaus algorithm

    In mathematics, the Zassenhaus algorithm is a method to calculate a basis for the intersection and sum of two subspaces of a vector space. It is named after Hans Zassenhaus, but no publication of this algorithm by him is known. It is used in computer algebra systems. == Algorithm == === Input === Let V be a vector space and U, W two finite-dimensional subspaces of V with the following spanning sets: U = ⟨ u 1 , … , u n ⟩ {\displaystyle U=\langle u_{1},\ldots ,u_{n}\rangle } and W = ⟨ w 1 , … , w k ⟩ . {\displaystyle W=\langle w_{1},\ldots ,w_{k}\rangle .} Finally, let B 1 , … , B m {\displaystyle B_{1},\ldots ,B_{m}} be linearly independent vectors so that u i {\displaystyle u_{i}} and w i {\displaystyle w_{i}} can be written as u i = ∑ j = 1 m a i , j B j {\displaystyle u_{i}=\sum _{j=1}^{m}a_{i,j}B_{j}} and w i = ∑ j = 1 m b i , j B j . {\displaystyle w_{i}=\sum _{j=1}^{m}b_{i,j}B_{j}.} === Output === The algorithm computes the base of the sum U + W {\displaystyle U+W} and a base of the intersection U ∩ W {\displaystyle U\cap W} . === Algorithm === The algorithm creates the following block matrix of size ( ( n + k ) × ( 2 m ) ) {\displaystyle ((n+k)\times (2m))} : ( a 1 , 1 a 1 , 2 ⋯ a 1 , m a 1 , 1 a 1 , 2 ⋯ a 1 , m ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ a n , 1 a n , 2 ⋯ a n , m a n , 1 a n , 2 ⋯ a n , m b 1 , 1 b 1 , 2 ⋯ b 1 , m 0 0 ⋯ 0 ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ b k , 1 b k , 2 ⋯ b k , m 0 0 ⋯ 0 ) {\displaystyle {\begin{pmatrix}a_{1,1}&a_{1,2}&\cdots &a_{1,m}&a_{1,1}&a_{1,2}&\cdots &a_{1,m}\\\vdots &\vdots &&\vdots &\vdots &\vdots &&\vdots \\a_{n,1}&a_{n,2}&\cdots &a_{n,m}&a_{n,1}&a_{n,2}&\cdots &a_{n,m}\\b_{1,1}&b_{1,2}&\cdots &b_{1,m}&0&0&\cdots &0\\\vdots &\vdots &&\vdots &\vdots &\vdots &&\vdots \\b_{k,1}&b_{k,2}&\cdots &b_{k,m}&0&0&\cdots &0\end{pmatrix}}} Using elementary row operations, this matrix is transformed to the row echelon form. Then, it has the following shape: ( c 1 , 1 c 1 , 2 ⋯ c 1 , m ∙ ∙ ⋯ ∙ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ c q , 1 c q , 2 ⋯ c q , m ∙ ∙ ⋯ ∙ 0 0 ⋯ 0 d 1 , 1 d 1 , 2 ⋯ d 1 , m ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ 0 0 ⋯ 0 d ℓ , 1 d ℓ , 2 ⋯ d ℓ , m 0 0 ⋯ 0 0 0 ⋯ 0 ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ 0 0 ⋯ 0 0 0 ⋯ 0 ) {\displaystyle {\begin{pmatrix}c_{1,1}&c_{1,2}&\cdots &c_{1,m}&\bullet &\bullet &\cdots &\bullet \\\vdots &\vdots &&\vdots &\vdots &\vdots &&\vdots \\c_{q,1}&c_{q,2}&\cdots &c_{q,m}&\bullet &\bullet &\cdots &\bullet \\0&0&\cdots &0&d_{1,1}&d_{1,2}&\cdots &d_{1,m}\\\vdots &\vdots &&\vdots &\vdots &\vdots &&\vdots \\0&0&\cdots &0&d_{\ell ,1}&d_{\ell ,2}&\cdots &d_{\ell ,m}\\0&0&\cdots &0&0&0&\cdots &0\\\vdots &\vdots &&\vdots &\vdots &\vdots &&\vdots \\0&0&\cdots &0&0&0&\cdots &0\end{pmatrix}}} Here, ∙ {\displaystyle \bullet } stands for arbitrary numbers, and the vectors ( c p , 1 , c p , 2 , … , c p , m ) {\displaystyle (c_{p,1},c_{p,2},\ldots ,c_{p,m})} for every p ∈ { 1 , … , q } {\displaystyle p\in \{1,\ldots ,q\}} and ( d p , 1 , … , d p , m ) {\displaystyle (d_{p,1},\ldots ,d_{p,m})} for every p ∈ { 1 , … , ℓ } {\displaystyle p\in \{1,\ldots ,\ell \}} are nonzero. Then ( y 1 , … , y q ) {\displaystyle (y_{1},\ldots ,y_{q})} with y i := ∑ j = 1 m c i , j B j {\displaystyle y_{i}:=\sum _{j=1}^{m}c_{i,j}B_{j}} is a basis of U + W {\displaystyle U+W} and ( z 1 , … , z ℓ ) {\displaystyle (z_{1},\ldots ,z_{\ell })} with z i := ∑ j = 1 m d i , j B j {\displaystyle z_{i}:=\sum _{j=1}^{m}d_{i,j}B_{j}} is a basis of U ∩ W {\displaystyle U\cap W} . === Proof of correctness === First, we define π 1 : V × V → V , ( a , b ) ↦ a {\displaystyle \pi _{1}:V\times V\to V,(a,b)\mapsto a} to be the projection to the first component. Let H := { ( u , u ) ∣ u ∈ U } + { ( w , 0 ) ∣ w ∈ W } ⊆ V × V . {\displaystyle H:=\{(u,u)\mid u\in U\}+\{(w,0)\mid w\in W\}\subseteq V\times V.} Then π 1 ( H ) = U + W {\displaystyle \pi _{1}(H)=U+W} and H ∩ ( 0 × V ) = 0 × ( U ∩ W ) {\displaystyle H\cap (0\times V)=0\times (U\cap W)} . Also, H ∩ ( 0 × V ) {\displaystyle H\cap (0\times V)} is the kernel of π 1 | H {\displaystyle {\pi _{1}|}_{H}} , the projection restricted to H. Therefore, dim ⁡ ( H ) = dim ⁡ ( U + W ) + dim ⁡ ( U ∩ W ) {\displaystyle \dim(H)=\dim(U+W)+\dim(U\cap W)} . The Zassenhaus algorithm calculates a basis of H. In the first m columns of this matrix, there is a basis y i {\displaystyle y_{i}} of U + W {\displaystyle U+W} . The rows of the form ( 0 , z i ) {\displaystyle (0,z_{i})} (with z i ≠ 0 {\displaystyle z_{i}\neq 0} ) are obviously in H ∩ ( 0 × V ) {\displaystyle H\cap (0\times V)} . Because the matrix is in row echelon form, they are also linearly independent. All rows which are different from zero ( ( y i , ∙ ) {\displaystyle (y_{i},\bullet )} and ( 0 , z i ) {\displaystyle (0,z_{i})} ) are a basis of H, so there are dim ⁡ ( U ∩ W ) {\displaystyle \dim(U\cap W)} such z i {\displaystyle z_{i}} s. Therefore, the z i {\displaystyle z_{i}} s form a basis of U ∩ W {\displaystyle U\cap W} . == Example == Consider the two subspaces U = ⟨ ( 1 − 1 0 1 ) , ( 0 0 1 − 1 ) ⟩ {\displaystyle U=\left\langle \left({\begin{array}{r}1\\-1\\0\\1\end{array}}\right),\left({\begin{array}{r}0\\0\\1\\-1\end{array}}\right)\right\rangle } and W = ⟨ ( 5 0 − 3 3 ) , ( 0 5 − 3 − 2 ) ⟩ {\displaystyle W=\left\langle \left({\begin{array}{r}5\\0\\-3\\3\end{array}}\right),\left({\begin{array}{r}0\\5\\-3\\-2\end{array}}\right)\right\rangle } of the vector space R 4 {\displaystyle \mathbb {R} ^{4}} . Using the standard basis, we create the following matrix of dimension ( 2 + 2 ) × ( 2 ⋅ 4 ) {\displaystyle (2+2)\times (2\cdot 4)} : ( 1 − 1 0 1 1 − 1 0 1 0 0 1 − 1 0 0 1 − 1 5 0 − 3 3 0 0 0 0 0 5 − 3 − 2 0 0 0 0 ) . {\displaystyle \left({\begin{array}{rrrrrrrr}1&-1&0&1&&1&-1&0&1\\0&0&1&-1&&0&0&1&-1\\\\5&0&-3&3&&0&0&0&0\\0&5&-3&-2&&0&0&0&0\end{array}}\right).} Using elementary row operations, we transform this matrix into the following matrix: ( 1 0 0 0 ∙ ∙ ∙ ∙ 0 1 0 − 1 ∙ ∙ ∙ ∙ 0 0 1 − 1 ∙ ∙ ∙ ∙ 0 0 0 0 1 − 1 0 1 ) {\displaystyle \left({\begin{array}{rrrrrrrrr}1&0&0&0&&\bullet &\bullet &\bullet &\bullet \\0&1&0&-1&&\bullet &\bullet &\bullet &\bullet \\0&0&1&-1&&\bullet &\bullet &\bullet &\bullet \\\\0&0&0&0&&1&-1&0&1\end{array}}\right)} (Some entries have been replaced by " ∙ {\displaystyle \bullet } " because they are irrelevant to the result.) Therefore ( ( 1 0 0 0 ) , ( 0 1 0 − 1 ) , ( 0 0 1 − 1 ) ) {\displaystyle \left(\left({\begin{array}{r}1\\0\\0\\0\end{array}}\right),\left({\begin{array}{r}0\\1\\0\\-1\end{array}}\right),\left({\begin{array}{r}0\\0\\1\\-1\end{array}}\right)\right)} is a basis of U + W {\displaystyle U+W} , and ( ( 1 − 1 0 1 ) ) {\displaystyle \left(\left({\begin{array}{r}1\\-1\\0\\1\end{array}}\right)\right)} is a basis of U ∩ W {\displaystyle U\cap W} .

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  • Collective operation

    Collective operation

    Collective operations are building blocks for interaction patterns, that are often used in SPMD algorithms in the parallel programming context. Hence, there is an interest in efficient realizations of these operations. A realization of the collective operations is provided by the Message Passing Interface (MPI). == Definitions == In all asymptotic runtime functions, we denote the latency α {\displaystyle \alpha } (or startup time per message, independent of message size), the communication cost per word β {\displaystyle \beta } , the number of processing units p {\displaystyle p} and the input size per node n {\displaystyle n} . In cases where we have initial messages on more than one node we assume that all local messages are of the same size. To address individual processing units we use p i ∈ { p 0 , p 1 , … , p p − 1 } {\displaystyle p_{i}\in \{p_{0},p_{1},\dots ,p_{p-1}\}} . If we do not have an equal distribution, i.e. node p i {\displaystyle p_{i}} has a message of size n i {\displaystyle n_{i}} , we get an upper bound for the runtime by setting n = max ( n 0 , n 1 , … , n p − 1 ) {\displaystyle n=\max(n_{0},n_{1},\dots ,n_{p-1})} . A distributed memory model is assumed. The concepts are similar for the shared memory model. However, shared memory systems can provide hardware support for some operations like broadcast (§ Broadcast) for example, which allows convenient concurrent read. Thus, new algorithmic possibilities can become available. == Broadcast == The broadcast pattern is used to distribute data from one processing unit to all processing units, which is often needed in SPMD parallel programs to dispense input or global values. Broadcast can be interpreted as an inverse version of the reduce pattern (§ Reduce). Initially only root r {\displaystyle r} with i d {\displaystyle id} 0 {\displaystyle 0} stores message m {\displaystyle m} . During broadcast m {\displaystyle m} is sent to the remaining processing units, so that eventually m {\displaystyle m} is available to all processing units. Since an implementation by means of a sequential for-loop with p − 1 {\displaystyle p-1} iterations becomes a bottleneck, divide-and-conquer approaches are common. One possibility is to utilize a binomial tree structure with the requirement that p {\displaystyle p} has to be a power of two. When a processing unit is responsible for sending m {\displaystyle m} to processing units i . . j {\displaystyle i..j} , it sends m {\displaystyle m} to processing unit ⌈ ( i + j ) / 2 ⌉ {\displaystyle \left\lceil (i+j)/2\right\rceil } and delegates responsibility for the processing units ⌈ ( i + j ) / 2 ⌉ . . j {\displaystyle \left\lceil (i+j)/2\right\rceil ..j} to it, while its own responsibility is cut down to i . . ⌈ ( i + j ) / 2 ⌉ − 1 {\displaystyle i..\left\lceil (i+j)/2\right\rceil -1} . Binomial trees have a problem with long messages m {\displaystyle m} . The receiving unit of m {\displaystyle m} can only propagate the message to other units, after it received the whole message. In the meantime, the communication network is not utilized. Therefore pipelining on binary trees is used, where m {\displaystyle m} is split into an array of k {\displaystyle k} packets of size ⌈ n / k ⌉ {\displaystyle \left\lceil n/k\right\rceil } . The packets are then broadcast one after another, so that data is distributed fast in the communication network. Pipelined broadcast on balanced binary tree is possible in O ( α log ⁡ p + β n ) {\displaystyle {\mathcal {O}}(\alpha \log p+\beta n)} , whereas for the non-pipelined case it takes O ( ( α + β n ) log ⁡ p ) {\displaystyle {\mathcal {O}}((\alpha +\beta n)\log p)} cost. == Reduce == The reduce pattern is used to collect data or partial results from different processing units and to combine them into a global result by a chosen operator. Given p {\displaystyle p} processing units, message m i {\displaystyle m_{i}} is on processing unit p i {\displaystyle p_{i}} initially. All m i {\displaystyle m_{i}} are aggregated by ⊗ {\displaystyle \otimes } and the result is eventually stored on p 0 {\displaystyle p_{0}} . The reduction operator ⊗ {\displaystyle \otimes } must be associative at least. Some algorithms require a commutative operator with a neutral element. Operators like s u m {\displaystyle sum} , m i n {\displaystyle min} , m a x {\displaystyle max} are common. Implementation considerations are similar to broadcast (§ Broadcast). For pipelining on binary trees the message must be representable as a vector of smaller object for component-wise reduction. Pipelined reduce on a balanced binary tree is possible in O ( α log ⁡ p + β n ) {\displaystyle {\mathcal {O}}(\alpha \log p+\beta n)} . == All-Reduce == The all-reduce pattern (also called allreduce) is used if the result of a reduce operation (§ Reduce) must be distributed to all processing units. Given p {\displaystyle p} processing units, message m i {\displaystyle m_{i}} is on processing unit p i {\displaystyle p_{i}} initially. All m i {\displaystyle m_{i}} are aggregated by an operator ⊗ {\displaystyle \otimes } and the result is eventually stored on all p i {\displaystyle p_{i}} . Analog to the reduce operation, the operator ⊗ {\displaystyle \otimes } must be at least associative. All-reduce can be interpreted as a reduce operation with a subsequent broadcast (§ Broadcast). For long messages a corresponding implementation is suitable, whereas for short messages, the latency can be reduced by using a hypercube (Hypercube (communication pattern) § All-Gather/ All-Reduce) topology, if p {\displaystyle p} is a power of two. All-reduce can also be implemented with a butterfly algorithm and achieve optimal latency and bandwidth. All-reduce is possible in O ( α log ⁡ p + β n ) {\displaystyle {\mathcal {O}}(\alpha \log p+\beta n)} , since reduce and broadcast are possible in O ( α log ⁡ p + β n ) {\displaystyle {\mathcal {O}}(\alpha \log p+\beta n)} with pipelining on balanced binary trees. All-reduce implemented with a butterfly algorithm achieves the same asymptotic runtime. == Prefix-Sum/Scan == The prefix-sum or scan operation is used to collect data or partial results from different processing units and to compute intermediate results by an operator, which are stored on those processing units. It can be seen as a generalization of the reduce operation (§ Reduce). Given p {\displaystyle p} processing units, message m i {\displaystyle m_{i}} is on processing unit p i {\displaystyle p_{i}} . The operator ⊗ {\displaystyle \otimes } must be at least associative, whereas some algorithms require also a commutative operator and a neutral element. Common operators are s u m {\displaystyle sum} , m i n {\displaystyle min} and m a x {\displaystyle max} . Eventually processing unit p i {\displaystyle p_{i}} stores the prefix sum ⊗ i ′ <= i {\displaystyle \otimes _{i'<=i}} m i ′ {\displaystyle m_{i'}} . In the case of the so-called exclusive prefix sum, processing unit p i {\displaystyle p_{i}} stores the prefix sum ⊗ i ′ < i {\displaystyle \otimes _{i' Read more →

  • DPVweb

    DPVweb

    DPVweb is a database for virologists working on plant viruses combining taxonomic, bioinformatic and symptom data. == Description == DPVweb is a central web-based source of information about viruses, viroids and satellites of plants, fungi and protozoa. It provides comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. It makes use of a large database that also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. There are currently about 10,000 such sequences. For comparative purposes, DPVweb also contains a representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. For each curated sequence the database contains the start and end positions of each feature (gene, non-translated region, etc.), and these have been checked for accuracy. As far as possible, the nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for personal computers. == History == The Descriptions of Plant Viruses (DPVs) were first published by the Association of Applied Biologists in 1970 as a series of leaflets, each one written by an expert describing a particular plant virus. In 1998 all of the 354 DPVs published in paper were scanned, and converted into an electronic format in a database and distributed on CDROM. In 2001 the descriptions were made available on the new DPVweb site, providing open access to the now 400+ DPVs (currently 415) as well as taxonomic and sequence data on all plant viruses. == Uses == DPVweb is an aid to researchers in the field of plant virology as well as an educational resource for students of virology and molecular biology. The site provides a single point of access for all known plant virus genome sequences making it easy to collect these sequences together for further analysis and comparison. Sequence data from the DPVweb database have proved valuable for a number of projects: survey of codon usage bias amongst all plant viruses, two-way comparisons between comprehensive sets of sequences from the families Flexiviridae and Potyviridae that have helped inform taxonomy and clarify genus and species discrimination criteria, a survey and verification of the polyprotein cleavage sites within the family Potyviridae.

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  • Tom's Planner

    Tom's Planner

    Tom's Planner is a web-based tool and application service provider for project planning, management and collaboration. == History == Tom's Planner is based on Curaçao. In November 2009, it announced its public beta launch on TechCrunch and moved out of beta in August 2010. In 2013 Tom's Planner acquired its competitor Gantto. == Software == Tom's Planner is project management software that enables the creation of project schedules (Gantt charts) using a visual perspective. Tom's Planner uses the Freemium Business Model. Users can register for a free account or choose a paid version. Tom's Planner is available in five languages and is used by thousands of users on a daily basis in more than 100 countries worldwide. Customers range from fortune 500 companies to small mom-and-pop shops. == Reviews == Tom's Planner has been reviewed by PC World, TechCrunch, Lifehacker, and several other periodicals.

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  • UI data binding

    UI data binding

    UI data binding is a software design pattern to simplify development of GUI applications. UI data binding binds UI elements to an application domain model. Most frameworks employ the Observer pattern as the underlying binding mechanism. To work efficiently, UI data binding has to address input validation and data type mapping. A bound control is a widget whose value is tied or bound to a field in a recordset (e.g., a column in a row of a table). Changes made to data within the control are automatically saved to the database when the control's exit event triggers. == Example == == Data binding frameworks and tools == === Delphi === DSharp third-party data binding tool OpenWire Visual Live Binding - third-party visual data binding tool === Java === JFace Data Binding JavaFX Property === .NET === Windows Forms data binding overview WPF data binding overview Avalonia Unity 3D data binding framework (available in modifications for NGUI, iGUI and EZGUI libraries) === JavaScript === Angular AngularJS Backbone.js Ember.js Datum.js knockout.js Meteor, via its Blaze live update engine OpenUI5 React Vue.js

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  • Organizational metacognition

    Organizational metacognition

    Organizational metacognition is knowing what an organization knows, a concept related to metacognition, organizational learning, the learning organization and sensemaking. It is used to describe how organizations and teams develop an awareness of their own thinking, learning how to learn, where awareness of ignorance can motivate learning. The organizational deutero-learning concept identified by Argyris and Schon defines when organizations learn how to carry out single-loop and double-loop learning. It has also been described as learning how to learn through a process of collaborative inquiry and reflection (evaluative inquiry). "When an organization engages in deutero-learning its members learn about the previous context for learning. They reflect on and inquire into previous episodes of organizational learning, or failure to learn. They discover what they did that facilitated or inhibited learning, they invent new strategies for learning, they produce these strategies, and they evaluate and generalize what they have produced" Learning what facilitates and inhibits learning enables organizations to develop new strategies to develop their knowledge. For example, identification of a gap between perceived performance (such as satisfaction) and actual performance (outcomes) creates an awareness that makes the organization understand that learning needs to occur, driving appropriate changes to the environment and processes. == Learning prototypes == Wijnhoven (2001) grouped four learning prototypes that best meet learning needs, the match between these needs and learning norms dictating an organization's learning capabilities; deutero-learning is the acquisition of these capabilities. knowledge gap analysis classification of problems to select operationally required knowledge and skills coping with organizational tremors and jolts by anticipation, response and adjustments of behavioural repertoires decisional uncertainty measurement == Terminological ambiguities == Organizational metacognition and organizational deutero-learning have both been described as the concept or phenomenon where organizations learn how to learn. Argyris and Schon (1978) place deutero-learning into their cognitive theory of action framework, neglecting aspects of adaptive behaviour and context core to Bateson's (1972) original definitions. In order to resolve terminological ambiguities, Visser (2007) reviewed and reformulated the concept of deutero-learning as, "the behavioral adaptation to patterns of conditioning in relationships in organizational contexts, distinguishing it from meta-learning and planned learning" (pg. 659). == Significance == Organizational metacognition is considered a key norm to the prescriptive concept of the learning organization. Its significance has been recognized by industry, the military and in disaster response. == Examples in practice == Examples of poor metacognition (deutero-learning) have been described in knowledge network environments, "Knowledge networking is important to most competitive enterprises today. Enterprise knowledge is becoming ever more specialized in nature, so no single person or organization can know everything in detail. Hence addressing complex, multidisciplinary problems requires developing and accessing a network of knowledgeable people and organizations. The problem is, many otherwise knowledgeable people and organizations are not fully aware of their knowledge networks, and even more problematic, they are not aware that they are not aware. This focuses our attention toward organizational metacognition."

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  • Software intelligence

    Software intelligence

    Software intelligence is insight into the inner workings and structural condition of software assets produced by software designed to analyze database structure, software framework and source code to better understand and control complex software systems in information technology environments. Similarly to business intelligence (BI), software intelligence is produced by a set of software tools and techniques for the mining of data and the software's inner-structure. Results are automatically produced and feed a knowledge base containing technical documentation and blueprints of the innerworking of applications, and make it available to all to be used by business and software stakeholders to make informed decisions, measure the efficiency of software development organizations, communicate about the software health, prevent software catastrophes. == History == Software intelligence has been used by Kirk Paul Lafler, an American engineer, entrepreneur, and consultant, and founder of Software Intelligence Corporation in 1979. At that time, it was mainly related to SAS activities, in which he has been an expert since 1979. In the early 1980s, Victor R. Basili participated in different papers detailing a methodology for collecting valid software engineering data relating to software engineering, evaluation of software development, and variations. In 2004, different software vendors in software analysis started using the terms as part of their product naming and marketing strategy. Then in 2010, Ahmed E. Hassan and Tao Xie defined software intelligence as a "practice offering software practitioners up-to-date and pertinent information to support their daily decision-making processes and Software Intelligence should support decision-making processes throughout the lifetime of a software system". They go on by defining software intelligence as a "strong impact on modern software practice" for the upcoming decades. == Capabilities == Because of the complexity and wide range of components and subjects implied in software, software intelligence is derived from different aspects of software: Software composition is the construction of software application components. Components result from software coding, as well as the integration of the source code from external components: Open source, 3rd party components, or frameworks. Other components can be integrated using application programming interface call to libraries or services. Software architecture refers to the structure and organization of elements of a system, relations, and properties among them. Software flaws designate problems that can cause security, stability, resiliency, and unexpected results. There is no standard definition of software flaws but the most accepted is from The MITRE Corporation where common flaws are cataloged as Common Weakness Enumeration. Software grades assess attributes of the software. Historically, the classification and terminology of attributes have been derived from the ISO 9126-3 and the subsequent ISO 25000:2005 quality model. Software economics refers to the resource evaluation of software in the past, present, or future to make decisions and to govern. == Components == The capabilities of software intelligence platforms include an increasing number of components: Code analyzer to serve as an information basis for other software intelligence components identifying objects created by the programming language, external objects from Open source, third parties objects, frameworks, API, or services Graphical visualization and blueprinting of the inner structure of the software product or application considered including dependencies, from data acquisition (automated and real-time data capture, end-user entries) up to data storage, the different layers within the software, and the coupling between all elements. Navigation capabilities within components and impact analysis features List of flaws, architectural and coding violations, against standardized best practices, cloud blocker preventing migration to a Cloud environment, and rogue data-call entailing the security and integrity of software Grades or scores of the structural and software quality aligned with industry-standard like OMG, CISQ or SEI assessing the reliability, security, efficiency, maintainability, and scalability to cloud or other systems. Metrics quantifying and estimating software economics including work effort, sizing, and technical debt Industry references and benchmarking allowing comparisons between outputs of analysis and industry standards == User aspect == Some considerations must be made in order to successfully integrate the usage of software Intelligence systems in a company. Ultimately the software intelligence system must be accepted and utilized by the users in order for it to add value to the organization. If the system does not add value to the users' mission, they simply don't use it as stated by M. Storey in 2003. At the code level and system representation, software intelligence systems must provide a different level of abstractions: an abstract view for designing, explaining and documenting and a detailed view for understanding and analyzing the software system. At the governance level, the user acceptance for software intelligence covers different areas related to the inner functioning of the system as well as the output of the system. It encompasses these requirements: Comprehensive: missing information may lead to a wrong or inappropriate decision, as well as it is a factor influencing the user acceptance of a system. Accurate: accuracy depends on how the data is collected to ensure fair and indisputable opinion and judgment. Precise: precision is usually judged by comparing several measurements from the same or different sources. Scalable: lack of scalability in the software industry is a critical factor leading to failure. Credible: outputs must be trusted and believed. Deploy-able and usable. == Applications == Software intelligence has many applications in all businesses relating to the software environment, whether it is software for professionals, individuals, or embedded software. Depending on the association and the usage of the components, applications will relate to: Change and modernization: uniform documentation and blueprinting on all inner components, external code integrated, or call to internal or external components of the software Resiliency and security: measuring against industry standards to diagnose structural flaws in an IT environment. Compliance validation regarding security, specific regulations or technical matters. Decisions making and governance: Providing analytics about the software itself or stakeholders involved in the development of the software, e.g. productivity measurement to inform business and IT leaders about progress towards business goals. Assessment and Benchmarking to help business and IT leaders to make informed, fact-based decision about software. == Marketplace == Software intelligence is a high-level discipline and has been gradually growing covering the applications listed above. There are several markets driving the need for it: Application Portfolio Analysis (APA) aiming at improving the enterprise performance. Software Assessment for producing the software KPI and improving quality and productivity. Software security and resiliency measures and validation. Software evolution or legacy modernization, for which blueprinting the software systems are needed nor tools improving and facilitating modifications.

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  • Generatrix

    Generatrix

    In geometry, a generatrix () or describent is a point, curve or surface that, when moved along a given path, generates a new shape. The path directing the motion of the generatrix motion is called a directrix or dirigent. == Examples == A cone can be generated by moving a line (the generatrix) fixed at the future apex of the cone along a closed curve (the directrix); if that directrix is a circle perpendicular to the line connecting its center to the apex, the motion is rotation around a fixed axis and the resulting shape is a circular cone. The generatrix of a cylinder, a limiting case of a cone, is a line that is kept parallel to some axis.

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  • KiSAO

    KiSAO

    The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. KiSAO is part of the BioModels.net project and of the COMBINE initiative. == Structure == KiSAO consists of three main branches: simulation algorithm simulation algorithm characteristic simulation algorithm parameter The elements of each algorithm branch are linked to characteristic and parameter branches using has characteristic and has parameter relationships accordingly. The algorithm branch itself is hierarchically structured using relationships which denote that the descendant algorithms were derived from, or specify, more general ancestors.

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  • Car–Parrinello molecular dynamics

    Car–Parrinello molecular dynamics

    Car–Parrinello molecular dynamics (CPMD) refers to either a method used in molecular dynamics (also known as the Car–Parrinello method) or the computational chemistry software package used to implement this method. The CPMD method is one of the major methods for calculating ab initio molecular dynamics (ab initio MD or AIMD). Ab initio molecular dynamics (AIMD) is a computational method that uses first principles through quantum mechanics to simulate the motion of atoms in a system. It is a type of molecular dynamics (MD) simulation that does not rely on empirical potentials or force fields to describe the interactions between atoms, but rather calculates these interactions entirely from the electronic structure of the system using quantum mechanics. In an ab initio MD simulation, the total energy of the system is calculated at each time step using density functional theory (DFT), Hartree-Fock (HF), or other electronic structure calculation methods. The forces acting on each atom are then determined from the gradient of the energy with respect to the atomic coordinates, and the equations of motion are solved to predict the trajectory of the atoms. AIMD permits chemical bond breaking and forming events to occur and accounts for electronic polarization effect. Therefore, Ab initio MD simulations can be used to study a wide range of phenomena, including the structural, thermodynamic, and dynamic properties of materials and chemical reactions. They are particularly useful for systems that are not well described by empirical potentials or force fields, such as systems with strong electronic correlation or systems with many degrees of freedom. However, ab initio MD simulations are computationally demanding and require significant computational resources. The CPMD method is related to the more common Born–Oppenheimer molecular dynamics (BOMD) method in that the quantum mechanical effect of the electrons is included in the calculation of energy and forces for the classical motion of the nuclei. CPMD and BOMD are different types of AIMD. However, whereas BOMD treats the electronic structure problem within the time-independent Schrödinger equation, CPMD explicitly includes the electrons as active degrees of freedom, via (fictitious) dynamical variables. The software is a parallelized plane wave / pseudopotential implementation of density functional theory, particularly designed for ab initio molecular dynamics. == Car–Parrinello method == The Car–Parrinello method is a type of molecular dynamics, usually employing periodic boundary conditions, planewave basis sets, and density functional theory, proposed by Roberto Car and Michele Parrinello in 1985 while working at SISSA, who were subsequently awarded the Dirac Medal by ICTP in 2009. In contrast to Born–Oppenheimer molecular dynamics wherein the nuclear (ions) degree of freedom are propagated using ionic forces which are calculated at each iteration by approximately solving the electronic problem with conventional matrix diagonalization methods, the Car–Parrinello method explicitly introduces the electronic degrees of freedom as (fictitious) dynamical variables, writing an extended Lagrangian for the system which leads to a system of coupled equations of motion for both ions and electrons. In this way, an explicit electronic minimization at each time step, as done in Born–Oppenheimer MD, is not needed: after an initial standard electronic minimization, the fictitious dynamics of the electrons keeps them on the electronic ground state corresponding to each new ionic configuration visited along the dynamics, thus yielding accurate ionic forces. In order to maintain this adiabaticity condition, it is necessary that the fictitious mass of the electrons is chosen small enough to avoid a significant energy transfer from the ionic to the electronic degrees of freedom. This small fictitious mass in turn requires that the equations of motion are integrated using a smaller time step than the one (1–10 fs) commonly used in Born–Oppenheimer molecular dynamics. Currently, the CPMD method can be applied to systems that consist of a few tens or hundreds of atoms and access timescales on the order of tens of picoseconds. == General approach == In CPMD the core electrons are usually described by a pseudopotential and the wavefunction of the valence electrons are approximated by a plane wave basis set. The ground state electronic density (for fixed nuclei) is calculated self-consistently, usually using the density functional theory method. Kohn-Sham equations are often used to calculate the electronic structure, where electronic orbitals are expanded in a plane-wave basis set. Then, using that density, forces on the nuclei can be computed, to update the trajectories (using, e.g. the Verlet integration algorithm). In addition, however, the coefficients used to obtain the electronic orbital functions can be treated as a set of extra spatial dimensions, and trajectories for the orbitals can be calculated in this context. == Fictitious dynamics == CPMD is an approximation of the Born–Oppenheimer MD (BOMD) method. In BOMD, the electrons' wave function must be minimized via matrix diagonalization at every step in the trajectory. CPMD uses fictitious dynamics to keep the electrons close to the ground state, preventing the need for a costly self-consistent iterative minimization at each time step. The fictitious dynamics relies on the use of a fictitious electron mass (usually in the range of 400 – 800 a.u.) to ensure that there is very little energy transfer from nuclei to electrons, i.e. to ensure adiabaticity. Any increase in the fictitious electron mass resulting in energy transfer would cause the system to leave the ground-state BOMD surface. === Lagrangian === L = 1 2 ( ∑ I n u c l e i M I R ˙ I 2 + μ ∑ i o r b i t a l s ∫ d r | ψ ˙ i ( r , t ) | 2 ) − E [ { ψ i } , { R I } ] + ∑ i j Λ i j ( ∫ d r ψ i ψ j − δ i j ) , {\displaystyle {\mathcal {L}}={\frac {1}{2}}\left(\sum _{I}^{\mathrm {nuclei} }\ M_{I}{\dot {\mathbf {R} }}_{I}^{2}+\mu \sum _{i}^{\mathrm {orbitals} }\int d\mathbf {r} \ |{\dot {\psi }}_{i}(\mathbf {r} ,t)|^{2}\right)-E\left[\{\psi _{i}\},\{\mathbf {R} _{I}\}\right]+\sum _{ij}\Lambda _{ij}\left(\int d\mathbf {r} \ \psi _{i}\psi _{j}-\delta _{ij}\right),} where μ {\displaystyle \mu } is the fictitious mass parameter; E[{ψi},{RI}] is the Kohn–Sham energy density functional, which outputs energy values when given Kohn–Sham orbitals and nuclear positions. === Orthogonality constraint === ∫ d r ψ i ∗ ( r , t ) ψ j ( r , t ) = δ i j , {\displaystyle \int d\mathbf {r} \ \psi _{i}^{}(\mathbf {r} ,t)\psi _{j}(\mathbf {r} ,t)=\delta _{ij},} where δij is the Kronecker delta. === Equations of motion === The equations of motion are obtained by finding the stationary point of the Lagrangian under variations of ψi and RI, with the orthogonality constraint. M I R ¨ I = − ∇ I E [ { ψ i } , { R I } ] {\displaystyle M_{I}{\ddot {\mathbf {R} }}_{I}=-\nabla _{I}\,E\left[\{\psi _{i}\},\{\mathbf {R} _{I}\}\right]} μ ψ ¨ i ( r , t ) = − δ E δ ψ i ∗ ( r , t ) + ∑ j Λ i j ψ j ( r , t ) , {\displaystyle \mu {\ddot {\psi }}_{i}(\mathbf {r} ,t)=-{\frac {\delta E}{\delta \psi _{i}^{}(\mathbf {r} ,t)}}+\sum _{j}\Lambda _{ij}\psi _{j}(\mathbf {r} ,t),} where Λij is a Lagrangian multiplier matrix to comply with the orthonormality constraint. === Born–Oppenheimer limit === In the formal limit where μ → 0, the equations of motion approach Born–Oppenheimer molecular dynamics. == Software packages == There are a number of software packages available for performing AIMD simulations. Some of the most widely used packages include: CP2K: an open-source software package for AIMD. Quantum Espresso: an open-source package for performing DFT calculations. It includes a module for AIMD. VASP: a commercial software package for performing DFT calculations. It includes a module for AIMD. Gaussian: a commercial software package that can perform AIMD. NWChem: an open-source software package for AIMD. LAMMPS: an open-source software package for performing classical and ab initio MD simulations. SIESTA: an open-source software package for AIMD. ORCA: a general-purpose quantum chemistry package. == Applications == Studying the behavior of water across different environments, such as near a hydrophobic graphene sheet. Investigating the structure and dynamics of liquid water at ambient temperature. Solving the heat transfer problems (heat conduction and thermal radiation), such as in Si/Ge superlattices. Probing the proton transfer along hydrogen-bonds in different environments, such as in 1D water chains inside carbon nanotubes. Evaluating the critical point of crystals, composites, and solid-state materials, such as aluminum. Predicting and modelling different phases and phase transitions, such as in the amorphous phase of the phase-change memory material GeSbTe. Studying the combustion of combustibles, such as lignite-water systems. Measuring th

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  • International Philosophical Bibliography

    International Philosophical Bibliography

    The International Philosophical Bibliography (IPB), also known in French as Répertoire bibliographique de la philosophie (RBP), is a bibliographic database covering publications on the history of philosophy and continental philosophy. The database comprises records of publications in over 30 languages. Annually, about 12,000 records are added. The indexes include, among other elements, over 84,000 names of authors, editors, translators, reviewers, and collaborators, as well as more than 3,000 commentaries on philosophical works, making it the world's most complete index in Philosophy. Since 1934, the IPB has been developed by the Higher Institute of Philosophy at the University of Louvain (UCLouvain), first in Leuven and since 1978 in Louvain-la-Neuve. The online version was launched by Peeters Publishers in 1997 and continues to be updated quarterly.

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  • Fantavision

    Fantavision

    Fantavision is an animation program by Scott Anderson for the Apple II and published by Broderbund in 1985. Versions were released for the Apple IIGS (1987), Amiga (1988), and MS-DOS (1988). Fantavision allows the creation of vector graphics animations using the mouse and keyboard. The user creates frames, and the software generates the frames between them. Because this is done in real-time, it allows for creative exploration and quick changes. The program uses a graphical user interface in the style of the Macintosh with pull-down menus and black text on a white background. Advertisements claimed Fantavision a revolutionary breakthrough that brings the animation features of "tweening" and "transforming" to home computers. == Reception == Compute! in 1989 called Fantavision the best animation program for the IBM PC, although it noted the inability to draw curves. == Reviews == Games #70

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  • Ontology engineering

    Ontology engineering

    In computer science, information science and systems engineering, ontology engineering is a field which studies the methods and methodologies for building ontologies, which encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities of a given domain of interest. In a broader sense, this field also includes a knowledge construction of the domain using formal ontology representations such as OWL/RDF. A large-scale representation of abstract concepts such as actions, time, physical objects and beliefs would be an example of ontological engineering. Ontology engineering is one of the areas of applied ontology, and can be seen as an application of philosophical ontology. Core ideas and objectives of ontology engineering are also central in conceptual modeling. Ontology engineering aims at making explicit the knowledge contained within software applications, and within enterprises and business procedures for a particular domain. Ontology engineering offers a direction towards solving the inter-operability problems brought about by semantic obstacles, i.e. the obstacles related to the definitions of business terms and software classes. Ontology engineering is a set of tasks related to the development of ontologies for a particular domain. Automated processing of information not interpretable by software agents can be improved by adding rich semantics to the corresponding resources, such as video files. One of the approaches for the formal conceptualization of represented knowledge domains is the use of machine-interpretable ontologies, which provide structured data in, or based on, RDF, RDFS, and OWL. Ontology engineering is the design and creation of such ontologies, which can contain more than just the list of terms (controlled vocabulary); they contain terminological, assertional, and relational axioms to define concepts (classes), individuals, and roles (properties) (TBox, ABox, and RBox, respectively). Ontology engineering is a relatively new field of study concerning the ontology development process, the ontology life cycle, the methods and methodologies for building ontologies, and the tool suites and languages that support them. A common way to provide the logical underpinning of ontologies is to formalize the axioms with description logics, which can then be translated to any serialization of RDF, such as RDF/XML or Turtle. Beyond the description logic axioms, ontologies might also contain SWRL rules. The concept definitions can be mapped to any kind of resource or resource segment in RDF, such as images, videos, and regions of interest, to annotate objects, persons, etc., and interlink them with related resources across knowledge bases, ontologies, and LOD datasets. This information, based on human experience and knowledge, is valuable for reasoners for the automated interpretation of sophisticated and ambiguous contents, such as the visual content of multimedia resources. Application areas of ontology-based reasoning include, but are not limited to, information retrieval, automated scene interpretation, and knowledge discovery. == Languages == An ontology language is a formal language used to encode the ontology. There are a number of such languages for ontologies, both proprietary and standards-based: Common logic is ISO standard 24707, a specification for a family of ontology languages that can be accurately translated into each other. The Cyc project has its own ontology language called CycL, based on first-order predicate calculus with some higher-order extensions. The Gellish language includes rules for its own extension and thus integrates an ontology with an ontology language. IDEF5 is a software engineering method to develop and maintain usable, accurate, domain ontologies. KIF is a syntax for first-order logic that is based on S-expressions. Rule Interchange Format (RIF), F-Logic and its successor ObjectLogic combine ontologies and rules. OWL is a language for making ontological statements, developed as a follow-on from RDF and RDFS, as well as earlier ontology language projects including OIL, DAML and DAML+OIL. OWL is intended to be used over the World Wide Web, and all its elements (classes, properties and individuals) are defined as RDF resources, and identified by URIs. OntoUML is a well-founded language for specifying reference ontologies. SHACL (RDF SHapes Constraints Language) is a language for describing structure of RDF data. It can be used together with RDFS and OWL or it can be used independently from them. XBRL (Extensible Business Reporting Language) is a syntax for expressing business semantics. == Methodologies and tools == DOGMA KAON OntoClean HOZO Protégé (software) Large language models == In life sciences == Life sciences is flourishing with ontologies that biologists use to make sense of their experiments. For inferring correct conclusions from experiments, ontologies have to be structured optimally against the knowledge base they represent. The structure of an ontology needs to be changed continuously so that it is an accurate representation of the underlying domain. Recently, an automated method was introduced for engineering ontologies in life sciences such as Gene Ontology (GO), one of the most successful and widely used biomedical ontology. Based on information theory, it restructures ontologies so that the levels represent the desired specificity of the concepts. Similar information theoretic approaches have also been used for optimal partition of Gene Ontology. Given the mathematical nature of such engineering algorithms, these optimizations can be automated to produce a principled and scalable architecture to restructure ontologies such as GO. Open Biomedical Ontologies (OBO), a 2006 initiative of the U.S. National Center for Biomedical Ontology, provides a common 'foundry' for various ontology initiatives, amongst which are: The Generic Model Organism Project (GMOD) Gene Ontology Consortium Sequence Ontology Ontology Lookup Service The Plant Ontology Consortium Standards and Ontologies for Functional Genomics and more

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  • Physical schema

    Physical schema

    A physical data model (or database design) is a representation of a data design as implemented, or intended to be implemented, in a database management system. In the lifecycle of a project it typically derives from a logical data model, though it may be reverse-engineered from a given database implementation. A complete physical data model will include all the database artifacts required to create relationships between tables or to achieve performance goals, such as indexes, constraint definitions, linking tables, partitioned tables or clusters. Analysts can usually use a physical data model to calculate storage estimates; it may include specific storage allocation details for a given database system. As of 2012 seven main databases dominate the commercial marketplace: Informix, Oracle, Postgres, SQL Server, Sybase, IBM Db2 and MySQL. Other RDBMS systems tend either to be legacy databases or used within academia such as universities or further education colleges. Physical data models for each implementation would differ significantly, not least due to underlying operating-system requirements that may sit underneath them. For example: SQL Server runs only on Microsoft Windows operating-systems (Starting with SQL Server 2017, SQL Server runs on Linux. It's the same SQL Server database engine, with many similar features and services regardless of your operating system), while Oracle and MySQL can run on Solaris, Linux and other UNIX-based operating-systems as well as on Windows. This means that the disk requirements, security requirements and many other aspects of a physical data model will be influenced by the RDBMS that a database administrator (or an organization) chooses to use. == Physical schema == Physical schema is a term used in data management to describe how data is to be represented and stored (files, indices, etc.) in secondary storage using a particular database management system (DBMS) (e.g., Oracle RDBMS, Sybase SQL Server, etc.). In the ANSI/SPARC Architecture three schema approach, the internal schema is the view of data that involved data management technology. This is as opposed to an external schema that reflects an individual's view of the data, or the conceptual schema that is the integration of a set of external schemas. The logical schema was the way data were represented to conform to the constraints of a particular approach to database management. At that time the choices were hierarchical and network. Describing the logical schema, however, still did not describe how physically data would be stored on disk drives. That is the domain of the physical schema. Now logical schemas describe data in terms of relational tables and columns, object-oriented classes, and XML tags. A single set of tables, for example, can be implemented in numerous ways, up to and including an architecture where table rows are maintained on computers in different countries.

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