Latent space

A latent space, also known as a latent feature space or embedding space, is an embedding of a set of items within a manifold in which items resembling each other are positioned closer to one another. Position within the latent space can be viewed as being defined by a set of latent variables that emerge from the resemblances between the objects. In most cases, the dimensionality of the latent space is chosen to be lower than the dimensionality of the feature space from which the data points are drawn, making the construction of a latent space an example of dimensionality reduction, which can also be viewed as a form of data compression. Latent spaces are usually fit via machine learning, and they can then be used as feature spaces in machine learning models, including classifiers and other supervised predictors. The interpretation of latent spaces in machine learning models is an ongoing area of research, but achieving clear interpretations remains challenging. The black-box nature of these models often makes the latent space unintuitive, while its high-dimensional, complex, and nonlinear characteristics further complicate the task of understanding it. Analysis of the latent space geometry of diffusion models reveals a fractal structure of phase transitions in the latent space, characterized by abrupt changes in the Fisher information metric. Some visualization techniques have been developed to connect the latent space to the visual world, but there is often not a direct connection between the latent space interpretation and the model itself. Such techniques include t-distributed stochastic neighbor embedding (t-SNE), where the latent space is mapped to two dimensions for visualization. Latent space distances lack physical units, so the interpretation of these distances may depend on the application. == Embedding models == Several embedding models have been developed to perform this transformation to create latent space embeddings given a set of data items and a similarity function. These models learn the embeddings by leveraging statistical techniques and machine learning algorithms. Here are some commonly used embedding models: Word2Vec: Word2Vec is a popular embedding model used in natural language processing (NLP). It learns word embeddings by training a neural network on a large corpus of text. Word2Vec captures semantic and syntactic relationships between words, allowing for meaningful computations like word analogies. GloVe: GloVe (Global Vectors for Word Representation) is another widely used embedding model for NLP. It combines global statistical information from a corpus with local context information to learn word embeddings. GloVe embeddings are known for capturing both semantic and relational similarities between words. Siamese Networks: Siamese networks are a type of neural network architecture commonly used for similarity-based embedding. They consist of two identical subnetworks that process two input samples and produce their respective embeddings. Siamese networks are often used for tasks like image similarity, recommendation systems, and face recognition. Variational Autoencoders (VAEs): VAEs are generative models that simultaneously learn to encode and decode data. The latent space in VAEs acts as an embedding space. By training VAEs on high-dimensional data, such as images or audio, the model learns to encode the data into a compact latent representation. VAEs are known for their ability to generate new data samples from the learned latent space. == Multimodality == Multimodality refers to the integration and analysis of multiple modes or types of data within a single model or framework. Embedding multimodal data involves capturing relationships and interactions between different data types, such as images, text, audio, and structured data. Multimodal embedding models aim to learn joint representations that fuse information from multiple modalities, allowing for cross-modal analysis and tasks. These models enable applications like image captioning, visual question answering, and multimodal sentiment analysis. To embed multimodal data, specialized architectures such as deep multimodal networks or multimodal transformers are employed. These architectures combine different types of neural network modules to process and integrate information from various modalities. The resulting embeddings capture the complex relationships between different data types, facilitating multimodal analysis and understanding. == Applications == Embedding latent space and multimodal embedding models have found numerous applications across various domains: Information retrieval: Embedding techniques enable efficient similarity search and recommendation systems by representing data points in a compact space. Natural language processing: Word embeddings have revolutionized NLP tasks like sentiment analysis, machine translation, and document classification. Computer vision: Image and video embeddings enable tasks like object recognition, image retrieval, and video summarization. Recommendation systems: Embeddings help capture user preferences and item characteristics, enabling personalized recommendations. Healthcare: Embedding techniques have been applied to electronic health records, medical imaging, and genomic data for disease prediction, diagnosis, and treatment. Social systems: Embedding techniques can be used to learn latent representations of social systems such as internal migration systems, academic citation networks, and world trade networks.

Supertoroid

In geometry and computer graphics, a supertoroid or supertorus is usually understood to be a family of doughnut-like surfaces (technically, a topological torus) whose shape is defined by mathematical formulas similar to those that define the superellipsoids. The plural of "supertorus" is either supertori or supertoruses. The family was described and named by Alan Barr in 1994. Barr's supertoroids have been fairly popular in computer graphics as a convenient model for many objects, such as smooth frames for rectangular things. One quarter of a supertoroid can provide a smooth and seamless 90-degree joint between two superquadric cylinders. However, they are not algebraic surfaces (except in special cases). == Formulas == Alan Barr's supertoroids are defined by parametric equations similar to the trigonometric equations of the torus, except that the sine and cosine terms are raised to arbitrary powers. Namely, the generic point P(u, v) of the surface is given by P ( u , v ) = ( X ( u , v ) Y ( u , v ) Z ( u , v ) ) = ( ( a + C u s ) C v t ( b + C u s ) S v t S u s ) {\displaystyle P(u,v)=\left({\begin{array}{c}X(u,v)\\Y(u,v)\\Z(u,v)\end{array}}\right)=\left({\begin{array}{c}(a+C_{u}^{s})C_{v}^{t}\\(b+C_{u}^{s})S_{v}^{t}\\S_{u}^{s}\end{array}}\right)} where C θ ε = sgn ⁡ ( cos ⁡ θ ) | cos ⁡ θ | ε , S θ ε = sgn ⁡ ( sin ⁡ θ ) | sin ⁡ θ | ε , {\displaystyle {\begin{aligned}C_{\theta }^{\varepsilon }&=\operatorname {sgn} (\cos \theta )\,\left|\,\cos \theta \,\right|^{\varepsilon },\\S_{\theta }^{\varepsilon }&=\operatorname {sgn} (\sin \theta )\ \left|\,\sin \theta \ \right|^{\varepsilon },\end{aligned}}} sgn is the sign function, and the parameters u, v range from 0 to 360 degrees (0 to 2π radians). In these formulas, the parameter s > 0 controls the "squareness" of the vertical sections, t > 0 controls the squareness of the horizontal sections, and a, b ≥ 1 are the major radii in the x and y directions. With s = t = 1 and a = b = R one obtains the ordinary torus with major radius R and minor radius 1, with the center at the origin and rotational symmetry about the z-axis. In general, the supertorus defined as above spans the intervals: − ( a + 1 ) ≤ x ≤ + ( a + 1 ) − ( b + 1 ) ≤ y ≤ + ( b + 1 ) − 1 ≤ z ≤ + 1 {\displaystyle {\begin{array}{rcccl}-(a+1)&\leq &x&\leq &+(a+1)\\[4pt]-(b+1)&\leq &y&\leq &+(b+1)\\[4pt]-1&\leq &z&\leq &+1\end{array}}} The whole shape is symmetric about the planes x = 0, y = 0, and z = 0. The hole runs in the z direction and spans the intervals − ( a − 1 ) ≤ x ≤ + ( a − 1 ) − ( b − 1 ) ≤ y ≤ + ( b − 1 ) − ∞ ≤ z ≤ + ∞ {\displaystyle {\begin{array}{rcccl}-(a-1)&\leq &x&\leq &+(a-1)\\[4pt]-(b-1)&\leq &y&\leq &+(b-1)\\[4pt]-\infty &\leq &z&\leq &+\infty \end{array}}} A curve of constant u on this surface is a horizontal Lamé curve with exponent ⁠ 2 t , {\displaystyle {\tfrac {2}{t}},} ⁠ scaled in x and y and displaced in z. A curve of constant v, projected on the plane x = 0 or y = 0, is a Lamé curve with exponent ⁠ 2 s , {\displaystyle {\tfrac {2}{s}},} ⁠ scaled and horizontally shifted. If v = 0, the curve is planar and spans the intervals: a − 1 ≤ x ≤ a + 1 − 1 ≤ z ≤ + 1 {\displaystyle {\begin{array}{rcccl}a-1&\leq &x&\leq &a+1\\[4pt]-1&\leq &z&\leq &+1\end{array}}} and similarly if v = 90°, 180°, 270°. The curve is also planar if a = b. In general, if a ≠ b and v is not a multiple of 90 degrees, the curve of constant v will not be planar; and, conversely, a vertical plane section of the supertorus will not be a Lamé curve. The basic supertoroid shape defined above is often modified by non-uniform scaling to yield supertoroids of specific width, length, and vertical thickness. == Plotting code == The following GNU Octave code generates plots of a supertorus:

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.

Cultural algorithm

Cultural algorithms (CA) are a branch of evolutionary computation where there is a knowledge component that is called the belief space in addition to the population component. In this sense, cultural algorithms can be seen as an extension to a conventional genetic algorithm. Cultural algorithms were introduced by Reynolds (see references). == Belief space == The belief space of a cultural algorithm is divided into distinct categories. These categories represent different domains of knowledge that the population has of the search space. The belief space is updated after each iteration by the best individuals of the population. The best individuals can be selected using a fitness function that assesses the performance of each individual in population much like in genetic algorithms. === List of belief space categories === Normative knowledge A collection of desirable value ranges for the individuals in the population component e.g. acceptable behavior for the agents in population. Domain specific knowledge Information about the domain of the cultural algorithm problem is applied to. Situational knowledge Specific examples of important events - e.g. successful/unsuccessful solutions Temporal knowledge History of the search space - e.g. the temporal patterns of the search process Spatial knowledge Information about the topography of the search space == Population == The population component of the cultural algorithm is approximately the same as that of the genetic algorithm. == Communication protocol == Cultural algorithms require an interface between the population and belief space. The best individuals of the population can update the belief space via the update function. Also, the knowledge categories of the belief space can affect the population component via the influence function. The influence function can affect population by altering the genome or the actions of the individuals. == Pseudocode for cultural algorithms == Initialize population space (choose initial population) Initialize belief space (e.g. set domain specific knowledge and normative value-ranges) Repeat until termination condition is met Perform actions of the individuals in population space Evaluate each individual by using the fitness function Select the parents to reproduce a new generation of offspring Let the belief space alter the genome of the offspring by using the influence function Update the belief space by using the accept function (this is done by letting the best individuals to affect the belief space) == Applications == Various optimization problems Social simulation Real-parameter optimization

Yooreeka

Yooreeka is a library for data mining, machine learning, soft computing, and mathematical analysis. The project started with the code of the book "Algorithms of the Intelligent Web". Although the term "Web" prevailed in the title, in essence, the algorithms are valuable in any software application. It covers all major algorithms and provides many examples. Yooreeka 2.x is licensed under the Apache License rather than the somewhat more restrictive LGPL (which was the license of v1.x). The library is written 100% in the Java language. == Algorithms == The following algorithms are covered: Clustering Hierarchical—Agglomerative (e.g. MST single link; ROCK) and Divisive Partitional (e.g. k-means) Classification Bayesian Decision trees Neural Networks Rule based (via Drools) Recommendations Collaborative filtering Content based Search PageRank DocRank Personalization

ViBe

ViBe is a background subtraction algorithm which has been presented at the IEEE ICASSP 2009 conference and was refined in later publications. More precisely, it is a software module for extracting background information from moving images. It has been developed by Oliver Barnich and Marc Van Droogenbroeck of the Montefiore Institute, University of Liège, Belgium. ViBe is patented: the patent covers various aspects such as stochastic replacement, spatial diffusion, and non-chronological handling. ViBe is written in the programming language C, and has been implemented on CPU, GPU and FPGA. == Technical description == Source: === Pixel model and classification process === Many advanced techniques are used to provide an estimate of the temporal probability density function (pdf) of a pixel x. ViBe's approach is different, as it imposes the influence of a value in the polychromatic space to be limited to the local neighborhood. In practice, ViBe does not estimate the pdf, but uses a set of previously observed sample values as a pixel model. To classify a value pt(x), it is compared to its closest values among the set of samples. === Model update: Sample values lifespan policy === ViBe ensures a smooth exponentially decaying lifespan for the sample values that constitute the pixel models. This makes ViBe able to successfully deal with concomitant events with a single model of a reasonable size for each pixel. This is achieved by choosing, randomly, which sample to replace when updating a pixel model. Once the sample to be discarded has been chosen, the new value replaces the discarded sample. The pixel model that would result from the update of a given pixel model with a given pixel sample cannot be predicted since the value to be discarded is chosen at random. === Model update: Spatial Consistency === To ensure the spatial consistency of the whole image model and handle practical situations such as small camera movements or slowly evolving background objects, ViBe uses a technique similar to that developed for the updating process in which it chooses at random and update a pixel model in the neighborhood of the current pixel. By denoting NG(x) and p(x) respectively the spatial neighborhood of a pixel x and its value, and assuming that it was decided to update the set of samples of x by inserting p(x), then ViBe also use this value p(x) to update the set of samples of one of the pixels in the neighborhood NG(x), chosen at random. As a result, ViBe is able to produce spatially coherent results directly without the use of any post-processing method. === Model initialization === Although the model could easily recover from any type of initialization, for example by choosing a set of random values, it is convenient to get an accurate background estimate as soon as possible. Ideally a segmentation algorithm would like to be able to segment the video sequences starting from the second frame, the first frame being used to initialize the model. Since no temporal information is available prior to the second frame, ViBe populates the pixel models with values found in the spatial neighborhood of each pixel; more precisely, it initializes the background model with values taken randomly in each pixel neighborhood of the first frame. The background estimate is therefore valid starting from the second frame of a video sequence.

Supertoroid

Jpred

Cultural algorithm

Yooreeka

ViBe

Yooreeka

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