Metadata management

Metadata management involves managing metadata about other data, whereby this "other data" is generally referred to as content data. The term is used most often in relation to digital media, but older forms of metadata are catalogs, dictionaries, and taxonomies. For example, the Dewey Decimal Classification is a metadata management system developed in 1876 for libraries. == Metadata schema == Metadata management goes by the end-to-end process and governance framework for creating, controlling, enhancing, attributing, defining and managing a metadata schema, model or other structured aggregation system, either independently or within a repository and the associated supporting processes (often to enable the management of content). For web-based systems, URLs, images, video etc. may be referenced from a triples table of object, attribute and value. == Scope == With specific knowledge domains, the boundaries of the metadata for each must be managed, since a general ontology is not useful to experts in one field whose language is knowledge-domain specific. == Metadata Manager == In the process of developing a knowledge management solution, creating a metadata schema, and a system in which metadata is managed, a dedicated resource may be appointed to maintain adherence to metadata standards as defined by data owners as well as general best practice. This person is responsible for curation of the business and technical layers of the metadata schema, and commonly involved with strategy and implementation. A metadata manager is not required to master all aspects, or be involved with everything concerning the solution, but an understanding of as much of the process as possible to ensure a relevant schema is developed. == Metadata management over time == Managing the metadata in a knowledge management solution is an important step in a metadata strategy. It is part of the strategy to make sure that the metadata are complete, current and correct at any given time. Managing a metadata project is also about making sure that users of the system are aware of the possibilities allowed by a well-designed metadata system and how to maximize the benefits of metadata. Regularly monitoring the metadata to ensure that the schema remains relevant is advised. === Wikipedia metadata === Wikipedia is a project that actively manages metadata for its articles and files. For example, volunteer editors carefully curate new biographical articles based on the notability (claim to fame), name, birth, and/or death dates. Similarly, volunteer editors carefully curate new architectural articles based on name, municipality, or geo coordinates. When new articles with a valid alternate spelling are added to Wikipedia that match up to existing articles based on metadata, these are then manually checked and if needed, tagged for merging. When new articles are added that are considered out of scope or otherwise unfit for Wikipedia, these are nominated for deletion. To help keep track of metadata on Wikipedia, the new Wikimedia project Wikidata was established in 2012. Click on the pictures to view more metadata about these images:

Artificial intelligence in spirituality

Some users of artificial intelligence (AI) technologies, especially chatbots, may develop beliefs that AI has or can attain supernatural or spiritual powers. AI models such as ChatGPT are turned to for fortune telling, mysticism and remote viewing. Recent and sudden advances in large language models have led to folk myths about their origin or capabilities, as well as their deification or worship by some users. Tucker Carlson has made similar claims, including directly to Sam Altman. Pope Leo XIV advised priests against using LLM models when it came to the creation of sermons.

Triplet loss

Triplet loss is a machine learning loss function widely used in one-shot learning, a setting where models are trained to generalize effectively from limited examples. It was conceived by Google researchers for their prominent FaceNet algorithm for face detection. Triplet loss is designed to support metric learning. Namely, to assist training models to learn an embedding (mapping to a feature space) where similar data points are closer together and dissimilar ones are farther apart, enabling robust discrimination across varied conditions. In the context of face detection, data points correspond to images. == Definition == The loss function is defined using triplets of training points of the form ( A , P , N ) {\displaystyle (A,P,N)} . In each triplet, A {\displaystyle A} (called an "anchor point") denotes a reference point of a particular identity, P {\displaystyle P} (called a "positive point") denotes another point of the same identity in point A {\displaystyle A} , and N {\displaystyle N} (called a "negative point") denotes a point of an identity different from the identity in point A {\displaystyle A} and P {\displaystyle P} . Let x {\displaystyle x} be some point and let f ( x ) {\displaystyle f(x)} be the embedding of x {\displaystyle x} in the finite-dimensional Euclidean space. It shall be assumed that the L2-norm of f ( x ) {\displaystyle f(x)} is unity (the L2 norm of a vector X {\displaystyle X} in a finite dimensional Euclidean space is denoted by ‖ X ‖ {\displaystyle \Vert X\Vert } .) We assemble m {\displaystyle m} triplets of points from the training dataset. The goal of training here is to ensure that, after learning, the following condition (called the "triplet constraint") is satisfied by all triplets ( A ( i ) , P ( i ) , N ( i ) ) {\displaystyle (A^{(i)},P^{(i)},N^{(i)})} in the training data set: ‖ f ( A ( i ) ) − f ( P ( i ) ) ‖ 2 2 + α < ‖ f ( A ( i ) ) − f ( N ( i ) ) ‖ 2 2 {\displaystyle \Vert f(A^{(i)})-f(P^{(i)})\Vert _{2}^{2}+\alpha <\Vert f(A^{(i)})-f(N^{(i)})\Vert _{2}^{2}} The variable α {\displaystyle \alpha } is a hyperparameter called the margin, and its value must be set manually. In the FaceNet system, its value was set as 0.2. Thus, the full form of the function to be minimized is the following: L = ∑ i = 1 m max ( ‖ f ( A ( i ) ) − f ( P ( i ) ) ‖ 2 2 − ‖ f ( A ( i ) ) − f ( N ( i ) ) ‖ 2 2 + α , 0 ) {\displaystyle L=\sum _{i=1}^{m}\max {\Big (}\Vert f(A^{(i)})-f(P^{(i)})\Vert _{2}^{2}-\Vert f(A^{(i)})-f(N^{(i)})\Vert _{2}^{2}+\alpha ,0{\Big )}} == Intuition == A baseline for understanding the effectiveness of triplet loss is the contrastive loss, which operates on pairs of samples (rather than triplets). Training with the contrastive loss pulls embeddings of similar pairs closer together, and pushes dissimilar pairs apart. Its pairwise approach is greedy, as it considers each pair in isolation. Triplet loss innovates by considering relative distances. Its goal is that the embedding of an anchor (query) point be closer to positive points than to negative points (also accounting for the margin). It does not try to further optimize the distances once this requirement is met. This is approximated by simultaneously considering two pairs (anchor-positive and anchor-negative), rather than each pair in isolation. == Triplet "mining" == One crucial implementation detail when training with triplet loss is triplet "mining", which focuses on the smart selection of triplets for optimization. This process adds an additional layer of complexity compared to contrastive loss. A naive approach to preparing training data for the triplet loss involves randomly selecting triplets from the dataset. In general, the set of valid triplets of the form ( A ( i ) , P ( i ) , N ( i ) ) {\displaystyle (A^{(i)},P^{(i)},N^{(i)})} is very large. To speed-up training convergence, it is essential to focus on challenging triplets. In the FaceNet paper, several options were explored, eventually arriving at the following. For each anchor-positive pair, the algorithm considers only semi-hard negatives. These are negatives that violate the triplet requirement (i.e, are "hard"), but lie farther from the anchor than the positive (not too hard). Restated, for each A ( i ) {\displaystyle A^{(i)}} and P ( i ) {\displaystyle P^{(i)}} , they seek N ( i ) {\displaystyle N^{(i)}} such that: The rationale for this design choice is heuristic. It may appear puzzling that the mining process neglects "very hard" negatives (i.e., closer to the anchor than the positive). Experiments conducted by the FaceNet designers found that this often leads to a convergence to degenerate local minima. Triplet mining is performed at each training step, from within the sample points contained in the training batch (this is known as online mining), after embeddings were computed for all points in the batch. While ideally the entire dataset could be used, this is impractical in general. To support a large search space for triplets, the FaceNet authors used very large batches (1800 samples). Batches are constructed by selecting a large number of same-category sample points (40), and randomly selected negatives for them. == Extensions == Triplet loss has been extended to simultaneously maintain a series of distance orders by optimizing a continuous relevance degree with a chain (i.e., ladder) of distance inequalities. This leads to the Ladder Loss, which has been demonstrated to offer performance enhancements of visual-semantic embedding in learning to rank tasks. In Natural Language Processing, triplet loss is one of the loss functions considered for BERT fine-tuning in the SBERT architecture. Other extensions involve specifying multiple negatives (multiple negatives ranking loss).

Silhouette (clustering)

Silhouette is a method of interpretation and validation of consistency within clusters of data. The technique provides a succinct graphical representation of how well each object has been classified. It was proposed by Belgian statistician Peter Rousseeuw in 1987. The silhouette value is a measure of how similar an object is to its own cluster (cohesion) compared to other clusters (separation). The silhouette value ranges from −1 to +1, where a high value indicates that the object is well matched to its own cluster and poorly matched to neighboring clusters. If most objects have a high value, then the clustering configuration is appropriate. If many points have a low or negative value, then the clustering configuration may have too many or too few clusters. A clustering with an average silhouette width of over 0.7 is considered to be "strong", a value over 0.5 "reasonable", and over 0.25 "weak". However, with an increasing dimensionality of the data, it becomes difficult to achieve such high values because of the curse of dimensionality, as the distances become more similar. The silhouette score is specialized for measuring cluster quality when the clusters are convex-shaped, and may not perform well if the data clusters have irregular shapes or are of varying sizes. The silhouette value can be calculated with any distance metric, such as Euclidean distance or Manhattan distance. == Definition == Assume the data have been clustered via any technique, such as k-medoids or k-means, into k {\displaystyle k} clusters. For data point i ∈ C i {\displaystyle i\in C_{i}} (data point i {\displaystyle i} in the cluster C i {\displaystyle C_{i}} ), calculate a ( i ) {\displaystyle a(i)} , the average distance that i {\displaystyle i} is from all other points in that cluster: a ( i ) = 1 | C i | − 1 ∑ j ∈ C i , i ≠ j d ( i , j ) {\displaystyle a(i)={\frac {1}{|C_{i}|-1}}\sum _{j\in C_{i},i\neq j}d(i,j)} where | C i | {\displaystyle |C_{i}|} is the number of points belonging to cluster C i {\displaystyle C_{i}} , and d ( i , j ) {\displaystyle d(i,j)} is the distance between data points i {\displaystyle i} and j {\displaystyle j} in the cluster C i {\displaystyle C_{i}} (we divide by | C i | − 1 {\displaystyle |C_{i}|-1} because the distance d ( i , i ) {\displaystyle d(i,i)} is not included in the sum). a ( i ) {\displaystyle a(i)} can be interpreted as a measure of how well i {\displaystyle i} is assigned to its cluster (the smaller the value, the better the assignment). We then define the mean dissimilarity of point i {\displaystyle i} to some cluster C j {\displaystyle C_{j}} as the mean of the distance from i {\displaystyle i} to all points in C j {\displaystyle C_{j}} (where C j ≠ C i {\displaystyle C_{j}\neq C_{i}} ). For each data point i ∈ C i {\displaystyle i\in C_{i}} , we now define b ( i ) {\displaystyle b(i)} as the average distance between i {\displaystyle i} and the points in the closest cluster (hence: "min") that i {\displaystyle i} does not belong to: b ( i ) = min j ≠ i 1 | C j | ∑ l ∈ C j d ( i , l ) {\displaystyle b(i)=\min _{j\neq i}{\frac {1}{|C_{j}|}}\sum _{l\in C_{j}}d(i,l)} The cluster with the smallest mean dissimilarity is said to be the "neighboring cluster" of i {\displaystyle i} because it is the next best fit cluster for point i {\displaystyle i} . We now define a silhouette (value) of one data point i {\displaystyle i} s ( i ) = b ( i ) − a ( i ) max { a ( i ) , b ( i ) } {\displaystyle s(i)={\frac {b(i)-a(i)}{\max\{a(i),b(i)\}}}} , if | C i | > 1 {\displaystyle |C_{i}|>1} and s ( i ) = 0 {\displaystyle s(i)=0} , if | C i | = 1 {\displaystyle |C_{i}|=1} , which can also be written as s ( i ) = { 1 − a ( i ) b ( i ) , if a ( i ) < b ( i ) 0 , if a ( i ) = b ( i ) b ( i ) a ( i ) − 1 , if a ( i ) > b ( i ) {\displaystyle s(i)={\begin{cases}1-{\frac {a(i)}{b(i)}},&{\mbox{ if }}a(i)b(i)\\\end{cases}}} From the above definition, s ( i ) {\displaystyle s(i)} is bounded to the interval [ − 1 , 1 ] {\displaystyle [-1,1]} , i.e. − 1 ≤ s ( i ) ≤ 1. {\displaystyle -1\leq s(i)\leq 1.} Note that a ( i ) {\displaystyle a(i)} is not clearly defined for clusters with size = 1, in which case we set s ( i ) = 0 {\displaystyle s(i)=0} . This choice is arbitrary, but neutral in the sense that it is at the midpoint of the bounds, -1 and 1. For s ( i ) {\displaystyle s(i)} to be close to 1 we require a ( i ) ≪ b ( i ) {\displaystyle a(i)\ll b(i)} . As a ( i ) {\displaystyle a(i)} is a measure of how dissimilar i {\displaystyle i} is to its own cluster, a small value means it is well matched. Furthermore, a large b ( i ) {\displaystyle b(i)} implies that i {\displaystyle i} is badly matched to its neighbouring cluster. Thus an s ( i ) {\displaystyle s(i)} close to 1 means that the data is appropriately clustered. If s ( i ) {\displaystyle s(i)} is close to -1, then by the same logic we see that i {\displaystyle i} would be more appropriate if it was clustered in its neighbouring cluster. An s ( i ) {\displaystyle s(i)} near zero means that the datum is on the border of two natural clusters. The mean s ( i ) {\displaystyle s(i)} over all points of a cluster is a measure of how tightly grouped all the points in the cluster are. Thus the mean s ( i ) {\displaystyle s(i)} over all data of the entire dataset is a measure of how appropriately the data have been clustered. If there are too many or too few clusters, as may occur when a poor choice of k {\displaystyle k} is used in the clustering algorithm (e.g., k-means), some of the clusters will typically display much narrower silhouettes than the rest. Thus silhouette plots and means may be used to determine the natural number of clusters within a dataset. One can also increase the likelihood of the silhouette being maximized at the correct number of clusters by re-scaling the data using feature weights that are cluster specific. Kaufman et al. introduced the term silhouette coefficient for the maximum value of the mean s ( i ) {\displaystyle s(i)} over all data of the entire dataset, i.e., S C = max k s ~ ( k ) , {\displaystyle SC=\max _{k}{\tilde {s}}\left(k\right),} where s ~ ( k ) {\displaystyle {\tilde {s}}\left(k\right)} represents the mean s ( i ) {\displaystyle s(i)} over all data of the entire dataset for a specific number of clusters k {\displaystyle k} . The silhouette coefficient describes the best possible clustering possible for a given number of clusters, as measured by the highest average silhouette score for all points in the dataset. == Simplified and medoid silhouette == Computing the silhouette coefficient needs all O ( N 2 ) {\displaystyle {\mathcal {O}}(N^{2})} pairwise distances, making this evaluation much more costly than clustering with k-means. For a clustering with centers μ C I {\displaystyle \mu _{C_{I}}} for each cluster C I {\displaystyle C_{I}} , we can use the following simplified Silhouette for each point i ∈ C I {\displaystyle i\in C_{I}} instead, which can be computed using only O ( N k ) {\displaystyle {\mathcal {O}}(Nk)} distances: a ′ ( i ) = d ( i , μ C I ) {\displaystyle a'(i)=d(i,\mu _{C_{I}})} and b ′ ( i ) = min C J ≠ C I d ( i , μ C J ) {\displaystyle b'(i)=\min _{C_{J}\neq C_{I}}d(i,\mu _{C_{J}})} , which has the additional benefit that a ′ ( i ) {\displaystyle a'(i)} is always defined, then define accordingly the simplified silhouette and simplified silhouette coefficient s ′ ( i ) = b ′ ( i ) − a ′ ( i ) max { a ′ ( i ) , b ′ ( i ) } {\displaystyle s'(i)={\frac {b'(i)-a'(i)}{\max\{a'(i),b'(i)\}}}} S C ′ = max k 1 N ∑ i s ′ ( i ) {\displaystyle SC'=\max _{k}{\frac {1}{N}}\sum _{i}s'\left(i\right)} . If the cluster centers are medoids (as in k-medoids clustering) instead of arithmetic means (as in k-means clustering), this is also called the medoid-based silhouette or medoid silhouette. If every object is assigned to the nearest medoid (as in k-medoids clustering), we know that a ′ ( i ) ≤ b ′ ( i ) {\displaystyle a'(i)\leq b'(i)} , and hence s ′ ( i ) = b ′ ( i ) − a ′ ( i ) b ′ ( i ) = 1 − a ′ ( i ) b ′ ( i ) {\displaystyle s'(i)={\frac {b'(i)-a'(i)}{b'(i)}}=1-{\frac {a'(i)}{b'(i)}}} . == Silhouette clustering == Instead of using the average silhouette to evaluate a clustering obtained from, e.g., k-medoids or k-means, we can try to directly find a solution that maximizes the Silhouette. We do not have a closed form solution to maximize this, but it will usually be best to assign points to the nearest cluster as done by these methods. Van der Laan et al. proposed to adapt the standard algorithm for k-medoids, PAM, for this purpose and call this algorithm PAMSIL: Choose initial medoids by using PAM Compute the average silhouette of this initial solution For each pair of a medoid m and a non-medoid x swap m and x compute the average silhouette of the resulting solution remember the best swap un-swap m and x for the next iteration Perform the best swap and return to

Jpred

Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction, that has existed since 1998 in different versions. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 134 000 jobs per month and has carried out over 2 million predictions in total for users in 179 countries. == JPred 2 == The static HTML pages of JPred 2 are still available for reference. == JPred 3 == The JPred v3 followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References). This release added new functionality and fixed many bugs. The highlights are: New, friendlier user interface Retrained and optimised version of Jnet (v2) - mean secondary structure prediction accuracy of >81% Batch submission of jobs Better error checking of input sequences/alignments Predictions now (optionally) returned via e-mail Users may provide their own query names for each submission JPred now makes a prediction even when there are no PSI-BLAST hits to the query PS/PDF output now incorporates all the predictions == JPred 4 == The current version of JPred (v4) has the following improvements and updates incorporated: Retrained on the latest UniRef90 and SCOPe/ASTRAL version of Jnet (v2.3.1) - mean secondary structure prediction accuracy of >82%. Upgraded the Web Server to the latest technologies (Bootstrap framework, JavaScript) and updating the web pages – improving the design and usability through implementing responsive technologies. Added RESTful API and mass-submission and results retrieval scripts - resulting in peak throughput above 20,000 predictions per day. Added prediction jobs monitoring tools. Upgraded the results reporting – both, on the web-site, and through the optional email summary reports: improved batch submission, added results summary preview through Jalview results visualization summary in SVG and adding full multiple sequence alignments into the reports. Improved help-pages, incorporating tool-tips, and adding one-page step-by-step tutorials. Sequence residues are categorised or assigned to one of the secondary structure elements, such as alpha-helix, beta-sheet and coiled-coil. Jnet uses two neural networks for its prediction. The first network is fed with a window of 17 residues over each amino acid in the alignment plus a conservation number. It uses a hidden layer of nine nodes and has three output nodes, one for each secondary structure element. The second network is fed with a window of 19 residues (the result of first network) plus the conservation number. It has a hidden layer with nine nodes and has three output nodes.

Color reproduction

Color reproduction is an aspect of color science concerned with producing light spectra that evoke a desired color, either through additive (light emitting) or subtractive (surface color) models. It converts physical correlates of color perception (CIE 1931 XYZ color space tristimulus values and related quantities) into light spectra that can be experienced by observers. In this way, it is the opposite of colorimetry. It is concerned with the faithful reproduction of a color in one medium, with a color in another, so it is a central concept in color management and relies heavily on color calibration. For example, food packaging must be able to faithfully reproduce the colors of the foods therein in order to appeal to a customer. This involves proper color calibration of at least four devices: Lighting, which must have a high color rendering index and not give a color cast to the object. Camera, which measures the reflected spectrum of the object and converts to a trichromatic color space (e.g. RGB). Screen, which reproduces color so a designer can proof the captured image and make color corrections as necessary. Printer, which reproduces the final color on paper.

Optimal discriminant analysis and classification tree analysis

Optimal Discriminant Analysis (ODA) and the related classification tree analysis (CTA) are exact statistical methods that maximize predictive accuracy. For any specific sample and exploratory or confirmatory hypothesis, optimal discriminant analysis (ODA) identifies the statistical model that yields maximum predictive accuracy, assesses the exact Type I error rate, and evaluates potential cross-generalizability. Optimal discriminant analysis may be applied to > 0 dimensions, with the one-dimensional case being referred to as UniODA and the multidimensional case being referred to as MultiODA. Optimal discriminant analysis is an alternative to ANOVA (analysis of variance) and regression analysis.