HKDF

HKDF is a multi-purpose key derivation function (KDF) based on the HMAC message authentication code. HKDF follows "extract-then-expand" paradigm, where the KDF logically consists of two modules: the first stage takes the input keying material and "extracts" from it a fixed-length pseudorandom key, and then the second stage "expands" this key into several additional, independent pseudorandom keys as the output of the KDF. == Mechanism == HKDF is the composition of two functions, HKDF-Extract and HKDF-Expand: HKDF(salt, IKM, info, length) = HKDF-Expand(HKDF-Extract(salt, IKM), info, length) === HKDF-Extract === HKDF-Extract (XTR) takes "input key material" or "source key material" (IKM or SKM) such as a shared secret generated using Diffie-Hellman; an optional, non-secret, random or pseudorandom salt (r); and generates a cryptographic key called the PRK ("pseudorandom key"). HKDF-Extract acts as a "randomness extractor", specifically a "computational extractor", taking a potentially non-uniform value of sufficient min-entropy and generating a value indistinguishable from a uniform random value (pseudorandom). Computational extractors assume attackers are computationally bounded and source entropy may only exist in a computational sense. Such extractors can be built using cryptographic functions under suitable assumptions, modeled as universal hash function (in the generic case) or a random oracle (in constrained scenarios like sources with weak entropy). Salt (r) acts as a "source-independent extractor", strengthening HKDF's security guarantees. Using a fixed public r is safe for multiple invocations of HKDF (on "independent" but secret IKMs which may or may not be derived from the same source), provided r isn't chosen or manipulated by an attacker. Ideally, r is a random string of hash function's output length. Even low quality r (weak entropy or shorter length) is recommended as they contribute "significantly" to the security of the OKM. Without or with a low-entropy, non-secret r, if an attacker can influence the IKMs source in a way that specifically exploits HKDF-Extract's underlying hash function (finding a collision or a specific bias), XTR provides no protection. A random r, even if fixed by the application (for example, random number generators using r as seed), would strengthen protections for that specific extractor session. In such a setting, sufficiently long IKMs also provide better entropy extraction. However, allowing the attacker to influence enough of the IKM after seeing r may result in a completely insecure KDF. HKDF-Extract is the result of HMAC with r as the key (all zeros up to length of the underlying extractor hash function, if not provided) and the IKM as the message. The underlying hash function used for HKDF-Extract step may be different to the one used by HKDF-Expand. It is recommended that HKDF-Extract uses strongest hash function available to the application, as it "concentrates" the entropy already present in IKM but may not necessarily "add" to it. Truncated output from a stronger underlying hash function for XTR (for example, SHA512/256) offers stronger extraction properties. The attacker is assumed to have partial knowledge about IKM (publicly known values in the case of Diffie-Hellman) or partial control over it (entropy pools). HKDF-Extract may be skipped if the IKM is itself a cryptographically strong key (and hence can assume the role of PRK), though it is recommended that HKDF-Extract be applied for the sake of compatibility with the general case, especially if r is available to the application. === HKDF-Expand === HKDF-Expand (PRF) takes the PRK (or any random key-derivation key if HKDF-Extract step is skipped), optional info (CTXinfo), and a length (L), to generate output key material (OKM) of length L. Multiple OKMs can be generated from a single PRK by using different values for CTXinfo, which must be "independent" of the IKM passed in HKDF-Extract. Even if an attacker, who knows r and some auxillary information about the secret IKM, can force the use of the same IKM (and PRK, by extension), in two or more HKDF-Expand contexts (represented by CTXinfo), the OKMs output are computationally independent (leak no useful information on each other). HKDF-Expand, acting as a variable-output-length pseudorandom function (PRF) keyed on PRK, calls HMAC on CTXinfo as the message (empty string, if unspecified) appended to a 8-bit counter i initialized to 1. Subsequent calls to HMAC are chained in "feedback mode" by prepending the previous HMAC output to CTXinfo and incrementing i. OKM is a function of the output size (k bits) of HMAC's underlying hash function; i.e., SHA-256 outputs OKM in segments of k=256 bits for up to a maximum of length i × k bits (255 × 256 bits = 8160 bytes) truncated to desired length L. HKDF-Expand may be skipped if PRK is at least desired length L, though it is recommended that HKDF-Expand be applied for additional "smoothing" of the OKM. == Standardization == HKDF was proposed as a building block in various protocols and applications, as well as to discourage the proliferation of multiple KDF mechanisms by its authors. It is formally described in RFC 5869 with detailed analysis in a paper published in 2010. NIST SP800-56Cr2 specifies a parameterizable extract-then-expand scheme, noting that RFC 5869 HKDF is a version of it and citing its paper for the rationale for the recommendations' extract-and-expand mechanisms. == Applications == HKDF is used in the Signal Protocol for end-to-end encrypted messaging where it generates the message keys, in conjunction with the triple Elliptic-curve Diffie-Hellman handshake (X3DH) key agreement protocol. Signal's "Secure Value Recovery" and "Sealed Sender" are based on HKDF. HKDF is a main component in the Noise Protocol Framework, Message Layer Security, and is used in widely deployed protocols like IPsec Internet Key Exchange and TLS 1.3. The "multi-purpose" nature of HKDF is meant to serve applications that require key extraction, key expansion, and key hierarchies in key wrapping, key exchange, PRNG, and password-based key derivation schemes. == Implementations == There are implementations of HKDF for C#, Go, Java, JavaScript, Perl, PHP, Python, Ruby, Rust, and other programming languages. RFC6234 lays out a reference C implementation of HKDF based on the Secure Hash Standard. === Example in Python ===

InciWeb

InciWeb is an interagency all-risk incident web information management system provided by the United States Forest Service released in 2004. It was originally developed for wildland fire emergencies, but can be also used for other emergency incidents (natural disasters, such as earthquakes, floods, hurricanes, and tornadoes). == Introduction == It was developed with two primary missions: 1. Provide the public a single source of incident related information 2. Provide a standardized reporting tool for the Public Affairs community Official announcements include evacuations, road closures, news releases, maps, photographs, and basic info and current situation about the incident. Incident information can be accessed by: web browser at https://inciweb.wildfire.gov/ Twitter RSS web feed == Technical == The original application was hosted at the United States Forest Service - Wildland Fire Training and Conference Center, at McClellan Airfield, California, comprising three servers: Database server Administrative server Load balancer for the public content which routes traffic to a pool of eight servers. Web traffic averages 2 million plus hits daily during the fire season with the ability to handle 3.5 million hits. The servers were moved to the National information Technology Center (NITC), Kansas City, Missouri on July 16, 2008, along with the release of version 2.0; the current version is 2.2. == Availability issues == InciWeb was having technical difficulties due to the high volume of Internet users trying to access the site during the September–October 2006 Day Fire and the Summer 2008 California wildfires. == Participating agencies == United States Forest Service Bureau of Land Management Bureau of Indian Affairs Fish and Wildlife Service National Park Service National Oceanic & Atmospheric Administration Department of the Interior Office of Aircraft Services National Association of State Foresters United States Fire Administration These same agencies are also in the National Interagency Fire Center.

Natural language understanding

Natural language understanding (NLU) or natural language interpretation (NLI) is a subset of natural language processing in artificial intelligence that deals with machine reading comprehension. NLU has been considered an AI-hard problem. There is considerable commercial interest in the field because of its application to automated reasoning, machine translation, question answering, news-gathering, text categorization, voice-activation, archiving, and large-scale content analysis. == History == The program STUDENT, written in 1964 by Daniel Bobrow for his PhD dissertation at MIT, is one of the earliest known attempts at NLU by a computer. Eight years after John McCarthy coined the term artificial intelligence, Bobrow's dissertation (titled Natural Language Input for a Computer Problem Solving System) showed how a computer could understand simple natural language input to solve algebra word problems. A year later, in 1965, Joseph Weizenbaum at MIT wrote ELIZA, an interactive program that carried on a dialogue in English on any topic, the most popular being psychotherapy. ELIZA worked by simple parsing and substitution of key words into canned phrases and Weizenbaum sidestepped the problem of giving the program a database of real-world knowledge or a rich lexicon. Yet ELIZA gained surprising popularity as a toy project and can be seen as a very early precursor to current commercial systems such as those used by Ask.com. In 1969, Roger Schank at Stanford University introduced the conceptual dependency theory for NLU. This model, partially influenced by the work of Sydney Lamb, was extensively used by Schank's students at Yale University, such as Robert Wilensky, Wendy Lehnert, and Janet Kolodner. In 1970, William A. Woods introduced the augmented transition network (ATN) to represent natural language input. Instead of phrase structure rules ATNs used an equivalent set of finite-state automata that were called recursively. ATNs and their more general format called "generalized ATNs" continued to be used for a number of years. In 1971, Terry Winograd finished writing SHRDLU for his PhD thesis at MIT. SHRDLU could understand simple English sentences in a restricted world of children's blocks to direct a robotic arm to move items. The successful demonstration of SHRDLU provided significant momentum for continued research in the field. Winograd continued to be a major influence in the field with the publication of his book Language as a Cognitive Process. At Stanford, Winograd would later advise Larry Page, who co-founded Google. In the 1970s and 1980s, the natural language processing group at SRI International continued research and development in the field. A number of commercial efforts based on the research were undertaken, e.g., in 1982 Gary Hendrix formed Symantec Corporation originally as a company for developing a natural language interface for database queries on personal computers. However, with the advent of mouse-driven graphical user interfaces, Symantec changed direction. A number of other commercial efforts were started around the same time, e.g., Larry R. Harris at the Artificial Intelligence Corporation and Roger Schank and his students at Cognitive Systems Corp. In 1983, Michael Dyer developed the BORIS system at Yale which bore similarities to the work of Roger Schank and W. G. Lehnert. The third millennium saw the introduction of systems using machine learning for text classification, such as the IBM Watson. However, experts debate how much "understanding" such systems demonstrate: e.g., according to John Searle, Watson did not even understand the questions. John Ball, cognitive scientist and inventor of the Patom Theory, supports this assessment. Natural language processing has made inroads for applications to support human productivity in service and e-commerce, but this has largely been made possible by narrowing the scope of the application. There are thousands of ways to request something in a human language that still defies conventional natural language processing. According to Wibe Wagemans, "To have a meaningful conversation with machines is only possible when we match every word to the correct meaning based on the meanings of the other words in the sentence – just like a 3-year-old does without guesswork." == Scope and context == The umbrella term "natural language understanding" can be applied to a diverse set of computer applications, ranging from small, relatively simple tasks such as short commands issued to robots, to highly complex endeavors such as the full comprehension of newspaper articles or poetry passages. Many real-world applications fall between the two extremes, for instance text classification for the automatic analysis of emails and their routing to a suitable department in a corporation does not require an in-depth understanding of the text, but needs to deal with a much larger vocabulary and more diverse syntax than the management of simple queries to database tables with fixed schemata. Throughout the years various attempts at processing natural language or English-like sentences presented to computers have taken place at varying degrees of complexity. Some attempts have not resulted in systems with deep understanding, but have helped overall system usability. For example, Wayne Ratliff originally developed the Vulcan program with an English-like syntax to mimic the English speaking computer in Star Trek. Vulcan later became the dBase system whose easy-to-use syntax effectively launched the personal computer database industry. Systems with an easy-to-use or English-like syntax are, however, quite distinct from systems that use a rich lexicon and include an internal representation (often as first order logic) of the semantics of natural language sentences. Hence the breadth and depth of "understanding" aimed at by a system determine both the complexity of the system (and the implied challenges) and the types of applications it can deal with. The "breadth" of a system is measured by the sizes of its vocabulary and grammar. The "depth" is measured by the degree to which its understanding approximates that of a fluent native speaker. At the narrowest and shallowest, English-like command interpreters require minimal complexity, but have a small range of applications. Narrow but deep systems explore and model mechanisms of understanding, but they still have limited application. Systems that attempt to understand the contents of a document such as a news release beyond simple keyword matching and to judge its suitability for a user are broader and require significant complexity, but they are still somewhat shallow. Systems that are both very broad and very deep are beyond the current state of the art. == Components and architecture == Regardless of the approach used, most NLU systems share some common components. The system needs a lexicon of the language and a parser and grammar rules to break sentences into an internal representation. The construction of a rich lexicon with a suitable ontology requires significant effort, e.g., the Wordnet lexicon required many person-years of effort. The system also needs theory from semantics to guide the comprehension. The interpretation capabilities of a language-understanding system depend on the semantic theory it uses. Competing semantic theories of language have specific trade-offs in their suitability as the basis of computer-automated semantic interpretation. These range from naive semantics or stochastic semantic analysis to the use of pragmatics to derive meaning from context. Semantic parsers convert natural-language texts into formal meaning representations. Advanced applications of NLU also attempt to incorporate logical inference within their framework. This is generally achieved by mapping the derived meaning into a set of assertions in predicate logic, then using logical deduction to arrive at conclusions. Therefore, systems based on functional languages such as Lisp need to include a subsystem to represent logical assertions, while logic-oriented systems such as those using the language Prolog generally rely on an extension of the built-in logical representation framework. The management of context in NLU can present special challenges. A large variety of examples and counter examples have resulted in multiple approaches to the formal modeling of context, each with specific strengths and weaknesses.

Condensation algorithm

The condensation algorithm (Conditional Density Propagation) is a computer vision algorithm. The principal application is to detect and track the contour of objects moving in a cluttered environment. Object tracking is one of the more basic and difficult aspects of computer vision and is generally a prerequisite to object recognition. Being able to identify which pixels in an image make up the contour of an object is a non-trivial problem. Condensation is a probabilistic algorithm that attempts to solve this problem. The algorithm itself is described in detail by Isard and Blake in a publication in the International Journal of Computer Vision in 1998. One of the most interesting facets of the algorithm is that it does not compute on every pixel of the image. Rather, pixels to process are chosen at random, and only a subset of the pixels end up being processed. Multiple hypotheses about what is moving are supported naturally by the probabilistic nature of the approach. The evaluation functions come largely from previous work in the area and include many standard statistical approaches. The original part of this work is the application of particle filter estimation techniques. The algorithm's creation was inspired by the inability of Kalman filtering to perform object tracking well in the presence of significant background clutter. The presence of clutter tends to produce probability distributions for the object state which are multi-modal and therefore poorly modeled by the Kalman filter. The condensation algorithm in its most general form requires no assumptions about the probability distributions of the object or measurements. == Algorithm overview == The condensation algorithm seeks to solve the problem of estimating the conformation of an object described by a vector x t {\displaystyle \mathbf {x_{t}} } at time t {\displaystyle t} , given observations z 1 , . . . , z t {\displaystyle \mathbf {z_{1},...,z_{t}} } of the detected features in the images up to and including the current time. The algorithm outputs an estimate to the state conditional probability density p ( x t | z 1 , . . . , z t ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {z_{1},...,z_{t}} )} by applying a nonlinear filter based on factored sampling and can be thought of as a development of a Monte-Carlo method. p ( x t | z 1 , . . . , z t ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {z_{1},...,z_{t}} )} is a representation of the probability of possible conformations for the objects based on previous conformations and measurements. The condensation algorithm is a generative model since it models the joint distribution of the object and the observer. The conditional density of the object at the current time p ( x t | z 1 , . . . , z t ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {z_{1},...,z_{t}} )} is estimated as a weighted, time-indexed sample set { s t ( n ) , n = 1 , . . . , N } {\displaystyle \{s_{t}^{(n)},n=1,...,N\}} with weights π t ( n ) {\displaystyle \pi _{t}^{(n)}} . N is a parameter determining the number of sample sets chosen. A realization of p ( x t | z 1 , . . . , z t ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {z_{1},...,z_{t}} )} is obtained by sampling with replacement from the set s t {\displaystyle s_{t}} with probability equal to the corresponding element of π t {\displaystyle \pi _{t}} . The assumptions that object dynamics form a temporal Markov chain and that observations are independent of each other and the dynamics facilitate the implementation of the condensation algorithm. The first assumption allows the dynamics of the object to be entirely determined by the conditional density p ( x t | x t − 1 ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {x_{t-1}} )} . The model of the system dynamics determined by p ( x t | x t − 1 ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {x_{t-1}} )} must also be selected for the algorithm, and generally includes both deterministic and stochastic dynamics. The algorithm can be summarized by initialization at time t = 0 {\displaystyle t=0} and three steps at each time t: === Initialization === Form the initial sample set and weights by sampling according to the prior distribution. For example, specify as Gaussian and set the weights equal to each other. === Iterative procedure === Sample with replacement N {\displaystyle N} times from the set { s 0 ( n ) , n = 1 , . . . , N } {\displaystyle \{s_{0}^{(n)},n=1,...,N\}} with probability { π 0 ( n ) , n = 1 , . . . , N } {\displaystyle \{\pi _{0}^{(n)},n=1,...,N\}} to generate a realization of p ( x t | z 1 , . . . , z t ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {z_{1},...,z_{t}} )} . Apply the learned dynamics p ( x t | x t − 1 ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {x_{t-1}} )} to each element of this new set, to generate a new set { s t ( n ) } {\displaystyle \{s_{t}^{(n)}\}} . To take into account the current observation z t {\displaystyle \mathbf {z_{t}} } , set π t ( n ) = p ( z t | s ( n ) ) ∑ j = 1 N p ( z t | s ( j ) ) {\displaystyle \pi _{t}^{(n)}={\frac {p(\mathbf {z_{t}} |s^{(n)})}{\sum _{j=1}^{N}p(\mathbf {z_{t}} |s^{(j)})}}} for each element { s t ( n ) } {\displaystyle \{s_{t}^{(n)}\}} . This algorithm outputs the probability distribution p ( x t | z 1 , . . . , z t ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {z_{1},...,z_{t}} )} which can be directly used to calculate the mean position of the tracked object, as well as the other moments of the tracked object. Cumulative weights can instead be used to achieve a more efficient sampling. == Implementation considerations == Since object-tracking can be a real-time objective, consideration of algorithm efficiency becomes important. The condensation algorithm is relatively simple when compared to the computational intensity of the Ricatti equation required for Kalman filtering. The parameter N {\displaystyle N} , which determines the number of samples in the sample set, will clearly hold a trade-off in efficiency versus performance. One way to increase efficiency of the algorithm is by selecting a low degree of freedom model for representing the shape of the object. The model used by Isard 1998 is a linear parameterization of B-splines in which the splines are limited to certain configurations. Suitable configurations were found by analytically determining combinations of contours from multiple views, of the object in different poses, and through principal component analysis (PCA) on the deforming object. Isard and Blake model the object dynamics p ( x t | x t − 1 ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {x_{t-1}} )} as a second order difference equation with deterministic and stochastic components: p ( x t | x t − 1 ) ∝ e − 1 2 | | B − 1 ( ( x t − x ¯ ) − A ( x t − 1 − x ¯ ) ) | | 2 ) {\displaystyle p(\mathbf {x_{t}} |\mathbf {x_{t-1}} )\propto e^{-{\frac {1}{2}}||B^{-1}((\mathbf {x_{t}} -\mathbf {\bar {x}} )-A(\mathbf {x_{t-1}} -\mathbf {\bar {x}} ))||^{2})}} where x ¯ {\displaystyle \mathbf {\bar {x}} } is the mean value of the state, and A {\displaystyle A} , B {\displaystyle B} are matrices representing the deterministic and stochastic components of the dynamical model respectively. A {\displaystyle A} , B {\displaystyle B} , and x ¯ {\displaystyle \mathbf {\bar {x}} } are estimated via Maximum Likelihood Estimation while the object performs typical movements. The observation model p ( z | x ) {\displaystyle p(\mathbf {z} |\mathbf {x} )} cannot be directly estimated from the data, requiring assumptions to be made in order to estimate it. Isard 1998 assumes that the clutter which may make the object not visible is a Poisson random process with spatial density λ {\displaystyle \lambda } and that any true target measurement is unbiased and normally distributed with standard deviation σ {\displaystyle \sigma } . The basic condensation algorithm is used to track a single object in time. It is possible to extend the condensation algorithm using a single probability distribution to describe the likely states of multiple objects to track multiple objects in a scene at the same time. Since clutter can cause the object probability distribution to split into multiple peaks, each peak represents a hypothesis about the object configuration. Smoothing is a statistical technique of conditioning the distribution based on both past and future measurements once the tracking is complete in order to reduce the effects of multiple peaks. Smoothing cannot be directly done in real-time since it requires information of future measurements. == Applications == The algorithm can be used for vision-based robot localization of mobile robots. Instead of tracking the position of an object in the scene, however, the position of the camera platform is tracked. This allows the camera platform to be globally localized given a visual map of the environment. Extensions of the condensation algorithm have also been used to recognize human gestures in image sequences. This application of the condensation algorithm impacts the ran

Hard sigmoid

In artificial intelligence, especially computer vision and artificial neural networks, a hard sigmoid is non-smooth function used in place of a sigmoid function. These retain the basic shape of a sigmoid, rising from 0 to 1, but using simpler functions, especially piecewise linear functions or piecewise constant functions. These are preferred where speed of computation is more important than precision. == Examples == The most extreme examples are the sign function or Heaviside step function, which go from −1 to 1 or 0 to 1 (which to use depends on normalization) at 0. Other examples include the Theano library, which provides two approximations: ultra_fast_sigmoid, which is a multi-part piecewise approximation and hard_sigmoid, which is a 3-part piecewise linear approximation (output 0, line with slope 0.2, output 1).

Single particle analysis

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

Hard sigmoid

In artificial intelligence, especially computer vision and artificial neural networks, a hard sigmoid is non-smooth function used in place of a sigmoid function. These retain the basic shape of a sigmoid, rising from 0 to 1, but using simpler functions, especially piecewise linear functions or piecewise constant functions. These are preferred where speed of computation is more important than precision. == Examples == The most extreme examples are the sign function or Heaviside step function, which go from −1 to 1 or 0 to 1 (which to use depends on normalization) at 0. Other examples include the Theano library, which provides two approximations: ultra_fast_sigmoid, which is a multi-part piecewise approximation and hard_sigmoid, which is a 3-part piecewise linear approximation (output 0, line with slope 0.2, output 1).