Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy (TEM). These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained particles are very noisy, making interpretation difficult. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features. An extension of this technique uses single particle methods to build up a three-dimensional reconstruction of the particle. Using cryo-electron microscopy it has become possible to generate reconstructions with sub-nanometer, near-atomic resolution resolution first in the case of highly symmetric viruses, and now in smaller, asymmetric proteins as well. == Techniques == Single particle analysis can be done on both negatively stained and vitreous ice-embedded transmission electron cryomicroscopy (CryoTEM) samples. Single particle analysis methods are, in general, reliant on the sample being homogeneous, although techniques for dealing with conformational heterogeneity are being developed. Images (micrographs) are taken with an electron microscope using charged-coupled device (CCD) detectors coupled to a phosphorescent layer (in the past, they were instead collected on film and digitized using high-quality scanners). The image processing is carried out using specialized software programs, often run on multi-processor computer clusters. Depending on the sample or the desired results, various steps of two- or three-dimensional processing can be done. === Alignment and classification === Biological samples, and especially samples embedded in thin vitreous ice, are highly radiation sensitive, thus only low electron doses can be used to image the sample. This low dose, as well as variations in the metal stain used (if used) means images have high noise relative to the signal given by the particle being observed. By aligning several similar images to each other so they are in register and then averaging them, an image with higher signal-to-noise ratio can be obtained. As the noise is mostly randomly distributed and the underlying image features constant, by averaging the intensity of each pixel over several images only the constant features are reinforced. Typically, the optimal alignment (a translation and an in-plane rotation) to map one image onto another is calculated by cross-correlation. However, a micrograph often contains particles in multiple different orientations and/or conformations, and so to get more representative image averages, a method is required to group similar particle images together into multiple sets. This is normally carried out using one of several data analysis and image classification algorithms, such as multi-variate statistical analysis and hierarchical ascendant classification, or k-means clustering. Often data sets of tens of thousands of particle images are used, and to reach an optimal solution an iterative procedure of alignment and classification is used, whereby strong image averages produced by classification are used as reference images for a subsequent alignment of the whole data set. === Image filtering === Image filtering (band-pass filtering) is often used to reduce the influence of high and/or low spatial frequency information in the images, which can affect the results of the alignment and classification procedures. This is particularly useful in negative stain images. The algorithms make use of fast Fourier transforms (FFT), often employing Gaussian shaped soft-edged masks in reciprocal space to suppress certain frequency ranges. High-pass filters remove low spatial frequencies (such as ramp or gradient effects), leaving the higher frequencies intact. Low-pass filters remove high spatial frequency features and have a blurring effect on fine details. === Contrast transfer function === Due to the nature of image formation in the electron microscope, bright-field TEM images are obtained using significant underfocus. This, along with features inherent in the microscope's lens system, creates blurring of the collected images visible as a point spread function. The combined effects of the imaging conditions are known as the contrast transfer function (CTF), and can be approximated mathematically as a function in reciprocal space. Specialized image processing techniques such as phase flipping and amplitude correction / Wiener filtering can (at least partially) correct for the CTF, and allow high resolution reconstructions. === Three-dimensional reconstruction === Transmission electron microscopy images are projections of the object showing the distribution of density through the object, similar to medical X-rays. By making use of the projection-slice theorem a three-dimensional reconstruction of the object can be generated by combining many images (2D projections) of the object taken from a range of viewing angles. Proteins in vitreous ice ideally adopt a random distribution of orientations (or viewing angles), allowing a fairly isotropic reconstruction if a large number of particle images are used. This contrasts with electron tomography, where the viewing angles are limited due to the geometry of the sample/imaging set up, giving an anisotropic reconstruction. Filtered back projection is a commonly used method of generating 3D reconstructions in single particle analysis, although many alternative algorithms exist. Before a reconstruction can be made, the orientation of the object in each image needs to be estimated. Several methods have been developed to work out the relative Euler angles of each image. Some are based on common lines (common 1D projections and sinograms), others use iterative projection matching algorithms. The latter works by beginning with a simple, low resolution 3D starting model and compares the experimental images to projections of the model and creates a new 3D to bootstrap towards a solution. Methods are also available for making 3D reconstructions of helical samples (such as tobacco mosaic virus), taking advantage of the inherent helical symmetry. Both real space methods (treating sections of the helix as single particles) and reciprocal space methods (using diffraction patterns) can be used for these samples. === Tilt methods === The specimen stage of the microscope can be tilted (typically along a single axis), allowing the single particle technique known as random conical tilt. An area of the specimen is imaged at both zero and at high angle (~60-70 degrees) tilts, or in the case of the related method of orthogonal tilt reconstruction, +45 and −45 degrees. Pairs of particles corresponding to the same object at two different tilts (tilt pairs) are selected, and by following the parameters used in subsequent alignment and classification steps a three-dimensional reconstruction can be generated relatively easily. This is because the viewing angle (defined as three Euler angles) of each particle is known from the tilt geometry. 3D reconstructions from random conical tilt suffer from missing information resulting from a restricted range of orientations. Known as the missing cone (due to the shape in reciprocal space), this causes distortions in the 3D maps. However, the missing cone problem can often be overcome by combining several tilt reconstructions. Tilt methods are best suited to negatively stained samples, and can be used for particles that adsorb to the carbon support film in preferred orientations. The phenomenon known as charging or beam-induced movement makes collecting high-tilt images of samples in vitreous ice challenging. === Map visualization and fitting === Various software programs are available that allow viewing the 3D maps. These often enable the user to manually dock in protein coordinates (structures from X-ray crystallography, NMR, or a computational model such as one found in the AlphaFold Protein Structure Database) of subunits into the electron density. Several programs can also fit subunits computationally; as of the 2020s using these programs tend to produce better accuracy than manual docking because they can perform labor-intensive tasks such as: The scale of SPA-derived maps depends on knowing the pixel size (angstorms per pixel), which is not always accurate. Programs can automatically correct for this difference by using coordinate data or by using knowledge of chemical bonds. Many proteins are made up of several roughly rigid protein domains linked by flexible parts. Pre-existing coordinate data, whether experimental or computational, may not exactly match the inter-domain positioning of the cyro-EM map. Modern programs can automatically "chop" pre-existing coordinate data into individual domains and fit them in individually. For higher-resolution structures, it is pos
Reciprocal human machine learning
Reciprocal Human Machine Learning (RHML) is an interdisciplinary approach to designing human-AI interaction systems. RHML aims to enable continual learning between humans and machine learning models by having them learn from each other. This approach keeps the human expert "in the loop" to oversee and enhance machine learning performance and simultaneously support the human expert continue learning. == Background == RHML emerged in the context of the rise of big data analytics and artificial intelligence for intelligent tasks like sense-making and decision-making. As machine learning advanced to take on more roles, researchers realized fully autonomous systems had limitations and needed human guidance. RHML extends the concept of human-in-the-loop systems by promoting reciprocal learning. Humans learn from their interactions with machine learning models, staying up-to-date on evolving technology. The models also learn from human feedback and oversight. This amplification of learning on both sides is a key focus of RHML. The approach draws on theories of learning in dyads from education and psychology. It also builds on human-computer interaction and human-centered design principles. Implementing RHML requires developing specialized tools and interfaces tailored to the application == Applications == RHML has been explored across diverse domains including: Cybersecurity - Software to enable reciprocal learning between experts and AI models for social media threat detection. Organizational decision-making - RHML to structure collaboration between humans and AI systems. Workplace training - Using RHML for workers to learn from AI technologies on the job. Open science - Using human and AI collaboration to promote open science. Production and logistics - turning workers and intelligent machines into teammates. RHML maintains human oversight and control over AI systems, while enabling cutting-edge machine learning performance. This collaborative approach highlights the importance of keeping the human expert involved in the loop. An example of RHML in application is Free Spirit (AFSFCV), an open-source architecture first published in early 2025 as a whitepaper, proposing a visually structured approach to intent-based human–AI interaction.
Umoove
Umoove is a high tech startup company that has developed and patented a software-only face and eye tracking technology. The idea was first conceived as an attempt to aid people with disabilities but has since evolved. The only compatibility qualification for tablet computers and smartphones to run Umoove software is a front-facing camera. Umoove headquarters are in Israel on Jerusalem’s Har Hotzvim. Umoove has 15 employees and received two million dollars in financing in 2012. The company's original founders invested around $800,000 to start the business in 2010. In 2013 Umoove was named one of the top three most promising Israeli start ups by Newsgeeks magazine. The company also participated in the 2013 LeWeb conference in Paris, France, where innovative technology startups are showcased. == Technology == The technology uses information extracted from previous frames, such as the angle of the user's head to predict where to look for facial targets in the next frame. This anticipation minimizes the amount of computation needed to scan each image. Umoove accounts for variances in environment, lighting conditions and user hand shake/movement. The technology is designed to provide a consistent experience, whether you're in a brightly lit area or a darkened basement, and to work fluidly between them by adapting its processing when it detects color and brightness shifts. It uses an active stabilization technique to filter out natural body movements from an unstable camera in order to minimize false-positive motion detection. Running the Umoove software on a Samsung Galaxy S3 is said to take up only 2% CPU. Umoove works exclusively with software and there is no hardware add-on necessary. It can be run on any smartphone or tablet computer that has a front-facing camera. Umoove claims that even a low-quality camera on an old device will run their software flawlessly. == Umoove Experience == In January 2014 Umoove released its first game onto the app store. The Umoove Experience game lets users control where they are 'flying' in the game through simple gestures and motions with their head. The avatar will basically go toward wherever the user looks. The game was created to showcase the technology for game developers but that did not stop some from criticizing its simplicity. Umoove also announced that they raised another one million dollars and that they are opening offices in Silicon Valley, California. In February 2014, Umoove announced that their face-tracking software development kit is available for Android developers as well as iOS. == Reviews == The Umoove Experience garnered mostly positive reviews from bloggers and mainstream media with some predicting that it could be the future of mobile gaming. Mashable wrote that Umoove's technology could be the emergence of gesture recognition technology in the mobile space, similar to Kinect with console gaming and what Leap Motion has done with desktop computers. Some, however, remain skeptical. CNET, for example, did not give the game a positive review and called the eye tracking technology 'freaky but cool'. They also noted that pioneering technologies have been known to fall short of expectations, citing Apple Inc’s Siri as an example. The technology blog GigaOM said that the Umoove Experience is ’awesome’ and technology evangelist Robert Scoble has called Umoove "brilliant". == uHealth == In January 2015, Umoove released uHealth, a mobile application that uses eye tracking game-like exercise to challenge the user's ability to be attentive, continuously focus, follow commands and avoid distractions. The app is designed in the form of two games, one to improve attention and another that hones focus. uHealth is a training tool, not a diagnostic. Umoove has stated that they want to use their technology for diagnosing neurological disorders but this will depend on clinical tests and FDA approval. The company cites the direct relationship between eye movements and brain activity as well as various vision-based therapies have been backed by many scientific studies conducted over the past decades. uHealth is the first time this type of therapy is delivered right to the end user through a simple download. == Collaboration rumors == In March 2013 there were rumors on the internet that Umoove would be the functioning software embedded into the Samsung Galaxy S4, which was due to launch that month. This rumor was perpetrated by, among others, New York Times, Techcrunch and Yahoo. Once Samsung launched without the Umoove technology rumors about a potential collaboration with Apple Inc hit the web. It has been said that due to the fact that Apple Inc is losing market share and stock value to Samsung they will be more aggressive and eye tracking is a logical place to make that move.
Object co-segmentation
In computer vision, object co-segmentation is a special case of image segmentation, which is defined as jointly segmenting semantically similar objects in multiple images or video frames. == Challenges == It is often challenging to extract segmentation masks of a target/object from a noisy collection of images or video frames, which involves object discovery coupled with segmentation. A noisy collection implies that the object/target is present sporadically in a set of images or the object/target disappears intermittently throughout the video of interest. Early methods typically involve mid-level representations such as object proposals. == Dynamic Markov networks-based methods == A joint object discover and co-segmentation method based on coupled dynamic Markov networks has been proposed recently, which claims significant improvements in robustness against irrelevant/noisy video frames. Unlike previous efforts which conveniently assumes the consistent presence of the target objects throughout the input video, this coupled dual dynamic Markov network based algorithm simultaneously carries out both the detection and segmentation tasks with two respective Markov networks jointly updated via belief propagation. Specifically, the Markov network responsible for segmentation is initialized with superpixels and provides information for its Markov counterpart responsible for the object detection task. Conversely, the Markov network responsible for detection builds the object proposal graph with inputs including the spatio-temporal segmentation tubes. == Graph cut-based methods == Graph cut optimization is a popular tool in computer vision, especially in earlier image segmentation applications. As an extension of regular graph cuts, multi-level hypergraph cut is proposed to account for more complex high order correspondences among video groups beyond typical pairwise correlations. With such hypergraph extension, multiple modalities of correspondences, including low-level appearance, saliency, coherent motion and high level features such as object regions, could be seamlessly incorporated in the hyperedge computation. In addition, as a core advantage over co-occurrence based approach, hypergraph implicitly retains more complex correspondences among its vertices, with the hyperedge weights conveniently computed by eigenvalue decomposition of Laplacian matrices. == CNN/LSTM-based methods == In action localization applications, object co-segmentation is also implemented as the segment-tube spatio-temporal detector. Inspired by the recent spatio-temporal action localization efforts with tubelets (sequences of bounding boxes), Le et al. present a new spatio-temporal action localization detector Segment-tube, which consists of sequences of per-frame segmentation masks. This Segment-tube detector can temporally pinpoint the starting/ending frame of each action category in the presence of preceding/subsequent interference actions in untrimmed videos. Simultaneously, the Segment-tube detector produces per-frame segmentation masks instead of bounding boxes, offering superior spatial accuracy to tubelets. This is achieved by alternating iterative optimization between temporal action localization and spatial action segmentation. The proposed segment-tube detector is illustrated in the flowchart on the right. The sample input is an untrimmed video containing all frames in a pair figure skating video, with only a portion of these frames belonging to a relevant category (e.g., the DeathSpirals). Initialized with saliency based image segmentation on individual frames, this method first performs temporal action localization step with a cascaded 3D CNN and LSTM, and pinpoints the starting frame and the ending frame of a target action with a coarse-to-fine strategy. Subsequently, the segment-tube detector refines per-frame spatial segmentation with graph cut by focusing on relevant frames identified by the temporal action localization step. The optimization alternates between the temporal action localization and spatial action segmentation in an iterative manner. Upon practical convergence, the final spatio-temporal action localization results are obtained in the format of a sequence of per-frame segmentation masks (bottom row in the flowchart) with precise starting/ending frames.
Production (computer science)
In computer science, a production or production rule is a rewrite rule that replaces some symbols with other symbols. A finite set of productions P {\displaystyle P} is the main component in the specification of a formal grammar (specifically a generative grammar). In such grammars, a set of productions is a special case of relation on the set of strings V ∗ {\displaystyle V^{}} (where ∗ {\displaystyle {}^{}} is the Kleene star operator) over a finite set of symbols V {\displaystyle V} called a vocabulary that defines which non-empty strings can be substituted with others. The set of productions is thus a special kind subset P ⊂ V ∗ × V ∗ {\displaystyle P\subset V^{}\times V^{}} and productions are then written in the form u → v {\displaystyle u\to v} to mean that ( u , v ) ∈ P {\displaystyle (u,v)\in P} (not to be confused with → {\displaystyle \to } being used as function notation, since there may be multiple rules for the same u {\displaystyle u} ). Given two subsets A , B ⊂ V ∗ {\displaystyle A,B\subset V^{}} , productions can be restricted to satisfy P ⊂ A × B {\displaystyle P\subset A\times B} , in which case productions are said "to be of the form A → B {\displaystyle A\to B} . Different choices and constructions of A , B {\displaystyle A,B} lead to different types of grammars. In general, any production of the form u → ϵ , {\displaystyle u\to \epsilon ,} where ϵ {\displaystyle \epsilon } is the empty string (sometimes also denoted λ {\displaystyle \lambda } ), is called an erasing rule, while productions that would produce strings out of nowhere, namely of the form ϵ → v , {\displaystyle \epsilon \to v,} are never allowed. In order to allow the production rules to create meaningful sentences, the vocabulary is partitioned into (disjoint) sets Σ {\displaystyle \Sigma } and N {\displaystyle N} providing two different roles: Σ {\displaystyle \Sigma } denotes the terminal symbols known as an alphabet containing the symbols allowed in a sentence; N {\displaystyle N} denotes nonterminal symbols, containing a distinguished start symbol S ∈ N {\displaystyle S\in N} , that are needed together with the production rules to define how to build the sentences. In the most general case of an unrestricted grammar, a production u → v {\displaystyle u\to v} , is allowed to map arbitrary strings u {\displaystyle u} and v {\displaystyle v} in V {\displaystyle V} (terminals and nonterminals), as long as u {\displaystyle u} is not empty. So unrestricted grammars have productions of the form V ∗ ∖ { ϵ } → V ∗ {\displaystyle V^{}\setminus \{\epsilon \}\to V^{}} or if we want to disallow changing finished sentences V ∗ N V ∗ = ( V ∗ ∖ Σ ∗ ) → V ∗ {\displaystyle V^{}NV^{}=(V^{}\setminus \Sigma ^{})\to V^{}} , where V ∗ N V ∗ {\displaystyle V^{}NV^{}} indicates concatenation and forces a non-terminal symbol to always be present on the left-hand side of the productions, and ∖ {\displaystyle \setminus } denotes set minus or set difference. If we do not allow the start symbol to occur in v {\displaystyle v} (the word on the right side), we have to replace V ∗ {\displaystyle V^{}} with ( V ∖ { S } ) ∗ {\displaystyle (V\setminus \{S\})^{}} on the right-hand side. The other types of formal grammar in the Chomsky hierarchy impose additional restrictions on what constitutes a production. Notably in a context-free grammar, the left-hand side of a production must be a single nonterminal symbol. So productions are of the form: N → V ∗ {\displaystyle N\to V^{}} == Grammar generation == To generate a string in the language, one begins with a string consisting of only a single start symbol, and then successively applies the rules (any number of times, in any order) to rewrite this string. This stops when a string containing only terminals is obtained. The language consists of all the strings that can be generated in this manner. Any particular sequence of legal choices taken during this rewriting process yields one particular string in the language. If there are multiple different ways of generating this single string, then the grammar is said to be ambiguous. For example, assume the alphabet consists of a {\displaystyle a} and b {\displaystyle b} , with the start symbol S {\displaystyle S} , and we have the following rules: 1. S → a S b {\displaystyle S\rightarrow aSb} 2. S → b a {\displaystyle S\rightarrow ba} then we start with S {\displaystyle S} , and can choose a rule to apply to it. If we choose rule 1, we replace S {\displaystyle S} with a S b {\displaystyle aSb} and obtain the string a S b {\displaystyle aSb} . If we choose rule 1 again, we replace S {\displaystyle S} with a S b {\displaystyle aSb} and obtain the string a a S b b {\displaystyle aaSbb} . This process is repeated until we only have symbols from the alphabet (i.e., a {\displaystyle a} and b {\displaystyle b} ). If we now choose rule 2, we replace S {\displaystyle S} with b a {\displaystyle ba} and obtain the string a a b a b b {\displaystyle aababb} , and are done. We can write this series of choices more briefly, using symbols: S ⇒ a S b ⇒ a a S b b ⇒ a a b a b b {\displaystyle S\Rightarrow aSb\Rightarrow aaSbb\Rightarrow aababb} . The language of the grammar is the set of all the strings that can be generated using this process: { b a , a b a b , a a b a b b , a a a b a b b b , … } {\displaystyle \{ba,abab,aababb,aaababbb,\dotsc \}} .
Averbis
Averbis has a focus on healthcare, pharma, automotive and intellectual property analytics. Averbis is involved in various research projects of the German Federal Ministry of Economics and Energy and the European Union such as DebugIT, EUCases, Mantra and SEMCARE. In addition to these projects, Averbis was also involved in the following projects: Greenpilot is a virtual library, which provides technical information in the fields of nutrition, environment and agriculture. Medpilot is a virtual library, which provides information about medicine and related sciences. In 2013, Averbis has been nominated for the German Founder Prize 2013. Averbis GmbH provides text analytics and text mining software to transform unstructured text into actionable information. It was founded in 2007 by IT experts after years of relevant scientific experience in the field of text mining and multilingual information retrieval. Averbis works in the field of terminology management, natural language processing, machine learning and semantic search. Its text mining software is embedded into the text mining framework UIMA.
Controlled natural language
Controlled natural languages (CNLs) are subsets of natural languages that are obtained by restricting the grammar and vocabulary in order to reduce or eliminate ambiguity and complexity. Traditionally, controlled languages fall into two major types: those that improve readability for human readers (e.g. non-native speakers), and those that enable reliable automatic semantic analysis of the language. The first type of languages (often called "simplified" or "technical" languages), for example ASD Simplified Technical English, Caterpillar Technical English, IBM's Easy English, are used in the industry to increase the quality of technical documentation, and possibly simplify the semi-automatic translation of the documentation. These languages restrict the writer by general rules such as "Keep sentences short", "Avoid the use of pronouns", "Only use dictionary-approved words", and "Use only the active voice". The second type of languages have a formal syntax and formal semantics, and can be mapped to an existing formal language, such as first-order logic. Thus, those languages can be used as knowledge representation languages, and writing of those languages is supported by fully automatic consistency and redundancy checks, query answering, etc. == Languages == Existing controlled natural languages include: == Encoding == IETF has reserved simple as a BCP 47 variant subtag for simplified versions of languages.