Design Automation usually refers to electronic design automation, or Design Automation which is a Product Configurator. Extending Computer-Aided Design (CAD), automated design and Computer-Automated Design (CAutoD) are more concerned with a broader range of applications, such as automotive engineering, civil engineering, composite material design, control engineering, dynamic system identification and optimization, financial systems, industrial equipment, mechatronic systems, steel construction, structural optimisation, and the invention of novel systems. The concept of CAutoD perhaps first appeared in 1963, in the IBM Journal of Research and Development, where a computer program was written. to search for logic circuits having certain constraints on hardware design to evaluate these logics in terms of their discriminating ability over samples of the character set they are expected to recognize. More recently, traditional CAD simulation is seen to be transformed to CAutoD by biologically-inspired machine learning, including heuristic search techniques such as evolutionary computation, and swarm intelligence algorithms. == Guiding designs by performance improvements == To meet the ever-growing demand of quality and competitiveness, iterative physical prototyping is now often replaced by 'digital prototyping' of a 'good design', which aims to meet multiple objectives such as maximised output, energy efficiency, highest speed and cost-effectiveness. The design problem concerns both finding the best design within a known range (i.e., through 'learning' or 'optimisation') and finding a new and better design beyond the existing ones (i.e., through creation and invention). This is equivalent to a search problem in an almost certainly, multidimensional (multivariate), multi-modal space with a single (or weighted) objective or multiple objectives. == Normalized objective function: cost vs. fitness == Using single-objective CAutoD as an example, if the objective function, either as a cost function J ∈ [ 0 , ∞ ) {\displaystyle J\in [0,\infty )} , or inversely, as a fitness function f ∈ ( 0 , 1 ] {\displaystyle f\in (0,1]} , where f = J 1 + J {\displaystyle f={\tfrac {J}{1+J}}} , is differentiable under practical constraints in the multidimensional space, the design problem may be solved analytically. Finding the parameter sets that result in a zero first-order derivative and that satisfy the second-order derivative conditions would reveal all local optima. Then comparing the values of the performance index of all the local optima, together with those of all boundary parameter sets, would lead to the global optimum, whose corresponding 'parameter' set will thus represent the best design. However, in practice, the optimization usually involves multiple objectives and the matters involving derivatives are a lot more complex. == Dealing with practical objectives == In practice, the objective value may be noisy or even non-numerical, and hence its gradient information may be unreliable or unavailable. This is particularly true when the problem is multi-objective. At present, many designs and refinements are mainly made through a manual trial-and-error process with the help of a CAD simulation package. Usually, such a posteriori learning or adjustments need to be repeated many times until a ‘satisfactory’ or ‘optimal’ design emerges. == Exhaustive search == In theory, this adjustment process can be automated by computerised search, such as exhaustive search. As this is an exponential algorithm, it may not deliver solutions in practice within a limited period of time. == Search in polynomial time == One approach to virtual engineering and automated design is evolutionary computation such as evolutionary algorithms. === Evolutionary algorithms === To reduce the search time, the biologically-inspired evolutionary algorithm (EA) can be used instead, which is a (non-deterministic) polynomial algorithm. The EA based multi-objective "search team" can be interfaced with an existing CAD simulation package in a batch mode. The EA encodes the design parameters (encoding being necessary if some parameters are non-numerical) to refine multiple candidates through parallel and interactive search. In the search process, 'selection' is performed using 'survival of the fittest' a posteriori learning. To obtain the next 'generation' of possible solutions, some parameter values are exchanged between two candidates (by an operation called 'crossover') and new values introduced (by an operation called 'mutation'). This way, the evolutionary technique makes use of past trial information in a similarly intelligent manner to the human designer. The EA based optimal designs can start from the designer's existing design database, or from an initial generation of candidate designs obtained randomly. A number of finely evolved top-performing candidates will represent several automatically optimized digital prototypes. There are websites that demonstrate interactive evolutionary algorithms for design. allows you to evolve 3D objects online and have them 3D printed. allows you to do the same for 2D images.
Matchbox Educable Noughts and Crosses Engine
The Matchbox Educable Noughts and Crosses Engine (sometimes called the Machine Educable Noughts and Crosses Engine or MENACE) was a mechanical computer made from 304 matchboxes designed and built by artificial intelligence researcher Donald Michie and his colleague Roger Chambers, in 1961. It was designed to play human opponents in games of noughts and crosses (tic-tac-toe) by returning a move for any given state of play and to refine its strategy through reinforcement learning. This was one of the first types of artificial intelligence. Michie and Chambers did not have immediate access to a computer; they worked around this by building the engine out of matchboxes. The matchboxes they used each represented a single possible layout of a noughts and crosses grid. When the computer first played, it would randomly choose moves based on the current layout. As it played more games, through a reinforcement loop, it disqualified strategies that led to losing games, and supplemented strategies that led to winning games. Michie held a tournament against MENACE in 1961, wherein he experimented with different openings. Following MENACE's maiden tournament against Michie, it demonstrated successful artificial intelligence in its strategy. Michie's essays on MENACE's weight initialisation and the BOXES algorithm used by MENACE became popular in the field of computer science research. Michie was honoured for his contribution to machine learning research, and was twice commissioned to program a MENACE simulation on an actual computer. == Origin == Donald Michie (1923–2007) had been on the team decrypting the German Tunny Code during World War II. Fifteen years later, he wanted to further display his mathematical and computational prowess with an early convolutional neural network. Since computer equipment was not obtainable for such uses, and Michie did not have a computer readily available, he decided to display and demonstrate artificial intelligence in a more esoteric format and constructed a functional mechanical computer out of matchboxes and beads. MENACE was constructed as the result of a bet with a computer science colleague who postulated that such a machine was impossible. Michie undertook the task of collecting and defining each matchbox as a "fun project", later turned into a demonstration tool. Michie completed his essay on MENACE in 1963, "Experiments on the mechanization of game-learning", as well as his essay on the BOXES Algorithm, written with R. A. Chambers and had built up an AI research unit in Hope Park Square, Edinburgh, Scotland. MENACE learned by playing successive matches of noughts and crosses. Each time, it would eliminate a losing strategy by the human player confiscating the beads that corresponded to each move. It reinforced winning strategies by making the moves more likely, by supplying extra beads. This was one of the earliest versions of the Reinforcement Loop, the schematic algorithm of looping the algorithm, dropping unsuccessful strategies until only the winning ones remain. This model starts as completely random, and gradually learns. == Composition == MENACE was made from 304 matchboxes glued together in an arrangement similar to a chest of drawers. Each box had a code number, which was keyed into a chart. This chart had drawings of tic-tac-toe game grids with various configurations of X, O, and empty squares, corresponding to all possible permutations a game could go through as it progressed. After removing duplicate arrangements (ones that were simply rotations or mirror images of other configurations), MENACE used 304 permutations in its chart and thus that many matchboxes. Each individual matchbox tray contained a collection of coloured beads. Each colour represented a move on a square on the game grid, and so matchboxes with arrangements where positions on the grid were already taken would not have beads for that position. Additionally, at the front of the tray were two extra pieces of card in a "V" shape, the point of the "V" pointing at the front of the matchbox. Michie and his artificial intelligence team called MENACE's algorithm "Boxes", after the apparatus used for the machine. The first stage "Boxes" operated in five phases, each setting a definition and a precedent for the rules of the algorithm in relation to the game. == Operation == MENACE played first, as O, since all matchboxes represented permutations only relevant to the "X" player. To retrieve MENACE's choice of move, the opponent or operator located the matchbox that matched the current game state, or a rotation or mirror image of it. For example, at the start of a game, this would be the matchbox for an empty grid. The tray would be removed and lightly shaken so as to move the beads around. Then, the bead that had rolled into the point of the "V" shape at the front of the tray was the move MENACE had chosen to make. Its colour was then used as the position to play on, and, after accounting for any rotations or flips needed based on the chosen matchbox configuration's relation to the current grid, the O would be placed on that square. Then the player performed their move, the new state was located, a new move selected, and so on, until the game was finished. When the game had finished, the human player observed the game's outcome. As a game was played, each matchbox that was used for MENACE's turn had its tray returned to it ajar, and the bead used kept aside, so that MENACE's choice of moves and the game states they belonged to were recorded. Michie described his reinforcement system with "reward" and "punishment". Once the game was finished, if MENACE had won, it would then receive a "reward" for its victory. The removed beads showed the sequence of the winning moves. These were returned to their respective trays, easily identifiable since they were slightly open, as well as three bonus beads of the same colour. In this way, in future games MENACE would become more likely to repeat those winning moves, reinforcing winning strategies. If it lost, the removed beads were not returned, "punishing" MENACE, and meaning that in future it would be less likely, and eventually incapable if that colour of bead became absent, to repeat the moves that cause a loss. If the game was a draw, one additional bead was added to each box. == Results in practice == === Optimal strategy === Noughts and crosses has a well-known optimal strategy. A player must place their symbol in a way that blocks the other player from achieving any rows while simultaneously making a row themself. However, if both players use this strategy, the game always ends in a draw. If the human player is familiar with the optimal strategy, and MENACE can quickly learn it, then the games will eventually only end in draws. The likelihood of the computer winning increases quickly when the computer plays against a random-playing opponent. When playing against a player using optimal strategy, the odds of a draw grow to 100%. In Donald Michie's official tournament against MENACE in 1961 he used optimal strategy, and he and the computer began to draw consistently after twenty games. Michie's tournament had the following milestones: Michie began by consistently opening with "Variant 0", the middle square. At 15 games, MENACE abandoned all non-corner openings. At just over 20, Michie switched to consistently using "Variant 1", the bottom-right square. At 60, he returned to Variant 0. As he neared 80 games, he moved to "Variant 2", the top-middle. At 110, he switched to "Variant 3", the top right. At 135, he switched to "Variant 4", middle-right. At 190, he returned to Variant 1, and at 210, he returned to Variant 0. The trend in changes of beads in the "2" boxes runs: === Correlation === Depending on the strategy employed by the human player, MENACE produces a different trend on scatter graphs of wins. Using a random turn from the human player results in an almost-perfect positive trend. Playing the optimal strategy returns a slightly slower increase. The reinforcement does not create a perfect standard of wins; the algorithm will draw random uncertain conclusions each time. After the j-th round, the correlation of near-perfect play runs: 1 − D D − D ( j + 2 ) ∑ i = 0 j D ( j i + 1 ) V i {\displaystyle {1-D \over D-D^{(j+2)}}\sum _{i=0}^{j}D^{(ji+1)}V_{i}} Where Vi is the outcome (+1 is win, 0 is draw and -1 is loss) and D is the decay factor (average of past values of wins and losses). Below, Mn is the multiplier for the n-th round of the game. == Legacy == Donald Michie's MENACE proved that a computer could learn from failure and success to become good at a task. It used what would become core principles within the field of machine learning before they had been properly theorised. For example, the combination of how MENACE starts with equal numbers of types of beads in each matchbox, and how these are then selected at random, creates a learning behaviour similar to weight initialisation
Navigational database
A navigational database is a type of database in which records or objects are found primarily by following references from other objects. The term was popularized by the title of Charles Bachman's 1973 Turing Award paper, The Programmer as Navigator. This paper emphasized the fact that the new disk-based database systems allowed the programmer to choose arbitrary navigational routes following relationships from record to record, contrasting this with the constraints of earlier magnetic-tape and punched card systems where data access was strictly sequential. One of the earliest navigational databases was Integrated Data Store (IDS), which was developed by Bachman for General Electric in the 1960s. IDS became the basis for the CODASYL database model in 1969. Although Bachman described the concept of navigation in abstract terms, the idea of navigational access came to be associated strongly with the procedural design of the CODASYL Data Manipulation Language. Writing in 1982, for example, Tsichritzis and Lochovsky state that "The notion of currency is central to the concept of navigation." By the notion of currency, they refer to the idea that a program maintains (explicitly or implicitly) a current position in any sequence of records that it is processing, and that operations such as GET NEXT and GET PRIOR retrieve records relative to this current position, while also changing the current position to the record that is retrieved. Navigational database programming thus came to be seen as intrinsically procedural; and moreover to depend on the maintenance of an implicit set of global variables (currency indicators) holding the current state. As such, the approach was seen as diametrically opposed to the declarative programming style used by the relational model. The declarative nature of relational languages such as SQL offered better programmer productivity and a higher level of data independence (that is, the ability of programs to continue working as the database structure evolves.) Navigational interfaces, as a result, were gradually eclipsed during the 1980s by declarative query languages. During the 1990s it started becoming clear that for certain applications handling complex data (for example, spatial databases and engineering databases), the relational calculus had limitations. At that time, a reappraisal of the entire database market began, with several companies describing the new systems using the marketing term NoSQL. Many of these systems introduced data manipulation languages which, while far removed from the CODASYL DML with its currency indicators, could be understood as implementing Bachman's "navigational" vision. Some of these languages are procedural; others (such as XPath) are entirely declarative. Offshoots of the navigational concept, such as the graph database, found new uses in modern transaction processing workloads. == Description == Navigational access is traditionally associated with the network model and hierarchical model of database, and conventionally describes data manipulation APIs in which records (or objects) are processed one at a time, iteratively. The essential characteristic as described by Bachman, however, is finding records by virtue of their relationship to other records: so an interface can still be navigational if it has set-oriented features. From this viewpoint, the key difference between navigational data manipulation languages and relational languages is the use of explicit named relationships rather than value-based joins: for department with name="Sales", find all employees in set department-employees versus find employees, departments where employee.department-code = department.code and department.name="Sales". In practice, however, most navigational APIs have been procedural: the above query would be executed using procedural logic along the lines of the following pseudo-code: On this viewpoint, the key difference between navigational APIs and the relational model (implemented in relational databases) is that relational APIs use "declarative" or logic programming techniques that ask the system what to fetch, while navigational APIs instruct the system in a sequence of steps how to reach the required records. Most criticisms of navigational APIs fall into one of two categories: Usability: application code quickly becomes unreadable and difficult to debug Data independence: application code needs to change whenever the data structure changes For many years the primary defence of navigational APIs was performance. Database systems that support navigational APIs often use internal storage structures that contain physical links or pointers from one record to another. While such structures may allow very efficient navigation, they have disadvantages because it becomes difficult to reorganize the physical placement of data. It is quite possible to implement navigational APIs without low-level pointer chasing (Bachman's paper envisaged logical relationships being implemented just as in relational systems, using primary keys and foreign keys), so the two ideas should not be conflated. But without the performance benefits of low-level pointers, navigational APIs become harder to justify. Hierarchical models often construct primary keys for records by concatenating the keys that appear at each level in the hierarchy. Such composite identifiers are found in computer file names (/usr/david/docs/index.txt), in URIs, in the Dewey decimal system, and for that matter in postal addresses. Such a composite key can be considered as representing a navigational path to a record; but equally, it can be considered as a simple primary key allowing associative access. As relational systems came to prominence in the 1980s, navigational APIs (and in particular, procedural APIs) were criticized and fell out of favour. The 1990s, however, brought a new wave of object-oriented databases that often provided both declarative and procedural interfaces. One explanation for this is that they were often used to represent graph-structured information (for example spatial data and engineering data) where access is inherently recursive: the mathematics originally underpinning SQL (specifically, first-order predicate calculus) does not have sufficient power to support recursive queries, even those as simple as a transitive closure. More recent SQL implementations do support hierarchical and recursive queries. A current example of a popular navigational API can be found in the Document Object Model (DOM) often used in web browsers and closely associated with JavaScript. The DOM is essentially an in-memory hierarchical database with an API that is both procedural and navigational. By contrast, the same data (XML or HTML) can be accessed using XPath, which can be categorized as declarative and navigational: data is accessed by following relationships, but the calling program does not issue a sequence of instructions to be followed in order. Languages such as SPARQL used to retrieve Linked Data from the Semantic Web are also simultaneously declarative and navigational. == Examples == IBM Information Management System IDMS
Pointer algorithm
In computer science, a pointer algorithm (sometimes called a pointer machine, or a reference machine; see the article Pointer machine for a close but non-identical concept) is a type of algorithm that manages a linked data structure. This concept is used as a model for lower-bound proofs and specific restrictions on the linked data structure and on the algorithm's access to the structure vary. This model has been used extensively with problems related to the disjoint-set data structure. Thus, Tarjan and La Poutré used this model to prove lower bounds on the amortized complexity of a disjoint-set data structure (La Poutré also addressed the interval split-find problem). Blum used this model to prove a lower bound on the single operation worst-case time of disjoint set data structure. Blum and Rochow proved a worst-case lower bound for the interval union-find problem. == Example == In Tarjan's lower bound for the disjoint set union problem, the assumptions on the algorithm are: The algorithm maintains a linked structure of nodes. Each element of the problem is associated with a node. Each set is represented by a node. The nodes of each set constitute a distinct connected component in the structure (this property is called separability). The find operation is performed by following links from the element node to the set node. Under these assumptions, the lower bound of Ω ( m α ( m , n ) ) {\displaystyle \Omega (m\alpha (m,n))} on the cost of a sequence of m operations is proven.
Applications of artificial intelligence
Artificial intelligence is the capability of computational systems to perform tasks that are typically associated with human intelligence, such as learning, reasoning, problem-solving, perception, and decision-making. Artificial intelligence has been used in applications throughout industry and academia. Within the field of Artificial Intelligence, there are multiple subfields. The subfield of machine learning has been used for various scientific and commercial purposes, including language translation, image recognition, decision-making, credit scoring, and e-commerce. In recent years, massive advancements have been made in the field of generative artificial intelligence, which uses generative models to generate text, images, videos, and other forms of data. This article describes applications of AI in different sectors. == Agriculture == In agriculture, AI has been proposed as a way for farmers to identify areas that need irrigation, fertilization, or pesticide treatments to increase yields, thereby improving efficiency. AI has been used to attempt to classify livestock pig call emotions, automate greenhouses, detect diseases and pests, and optimize irrigation. == AI-assisted software develoment == == Architecture and design == == Business == A 2023 study found that generative AI increased productivity by 15% in contact centers. Another 2023 study found it increased productivity by up to 40% in writing tasks. An August 2025 review by MIT found that of surveyed companies, 95% did not report any improvement in revenue from the use of AI. A September 2025 article by the Harvard Business Review describes how increased use of AI does not automatically lead to increases in revenue or actual productivity. Referring to "AI generated work content that masquerades as good work, but lacks the substance to meaningfully advance a given task" the article coins the term workslop. Per studies done in collaboration with the Stanford Social Media Lab, workslop does not improve productivity and undermines trust and collaboration among colleagues. In telehealth, agentic AI is reportedly facilitating the creation of large business models (millions in annual profit) with 1-2 employees, such as MEDVi, which as of August 2025 only had 2 employees and ~$75M in annual profit for GLP-1 weight-loss telehealth services. == Chatbots == == Computer science == === Programming assistance === ==== AI-assisted software development ==== AI can be used for real-time code completion, chat, and automated test generation. These tools are typically integrated with editors and IDEs as plugins. AI-assisted software development systems differ in functionality, quality, speed, and approach to privacy. Creating software primarily via AI is known as "vibe coding". Code created or suggested by AI can be incorrect or inefficient. The use of AI-assisted coding can potentially speed-up software development, but can also slow-down the process by creating more work when debugging and testing. The rush to prematurely adopt AI technology can also incur additional technical debt. AI also requires additional consideration and careful review for cybersecurity, since AI coding software is trained on a wide range of code of inconsistent quality and often replicates poor practices. ==== Neural network design ==== AI can be used to create other AIs. For example, around November 2017, Google's AutoML project to evolve new neural net topologies created NASNet, a system optimized for ImageNet and POCO F1. NASNet's performance exceeded all previously published performance on ImageNet. ==== Quantum computing ==== Research and development of quantum computers has been performed with machine learning algorithms. For example, there is a prototype, photonic, quantum memristive device for neuromorphic computers (NC)/artificial neural networks and NC-using quantum materials with some variety of potential neuromorphic computing-related applications. The use of quantum machine learning for quantum simulators has been proposed for solving physics and chemistry problems. === Historical contributions === AI researchers have created many tools to solve the most difficult problems in computer science. Many of their inventions have been adopted by mainstream computer science and are no longer considered AI. All of the following were originally developed in AI laboratories: Time sharing Interactive interpreters Graphical user interfaces and the computer mouse Rapid application development environments The linked list data structure Automatic storage management Symbolic programming Functional programming Dynamic programming Object-oriented programming Optical character recognition Constraint satisfaction == Customer service == === Human resources === AI programs have been used in hiring processes to screen resumes and rank candidates based on their qualifications, predict a candidate's likelihood of success in a given role, and automate repetitive communication tasks using chatbots. Studies on these programs have identified tendencies for gender bias, favoring male names and male-coded characteristics, as well as bias against disabled candidates and racial minorities. === Online and telephone customer service === AI underlies avatars (automated online assistants) on web pages. It can reduce operation and training costs. Pypestream automated customer service for its mobile application to streamline communication with customers. A Google app analyzes language and converts speech into text. The platform can identify angry customers through their language and respond appropriately. Amazon uses a chatbot for customer service that can perform tasks like checking the status of an order, cancelling orders, offering refunds and connecting the customer with a human representative. Generative AI (GenAI), such as ChatGPT, is increasingly used in business to automate tasks and enhance decision-making. === Hospitality === In the hospitality industry, AI is used to reduce repetitive tasks, analyze trends, interact with guests, and predict customer needs. AI hotel services come in the form of a chatbot, application, virtual voice assistant and service robots. == Education == In educational institutions, AI has been used to automate routine tasks such as attendance tracking, grading, and marking. AI tools have also been used to monitor student progress and analyze learning behaviors, with the goal of facilitating timely interventions for students facing academic challenges. == Energy and environment == === Energy system === The U.S. Department of Energy wrote in an April 2024 report that AI may have applications in modeling power grids, reviewing federal permits with large language models, predicting levels of renewable energy production, and improving the planning process for electrical vehicle charging networks. Other studies have suggested that machine learning can be used for energy consumption prediction and scheduling, e.g. to help with renewable energy intermittency management (see also: smart grid and climate change mitigation in the power grid). === Environmental monitoring === Autonomous ships that monitor the ocean, AI-driven satellite data analysis, passive acoustics or remote sensing and other applications of environmental monitoring make use of machine learning. For example, "Global Plastic Watch" is an AI-based satellite monitoring-platform for analysis/tracking of plastic waste sites to help prevention of plastic pollution – primarily ocean pollution – by helping identify who and where mismanages plastic waste, dumping it into oceans. === Early-warning systems === Machine learning can be used to spot early-warning signs of disasters and environmental issues, possibly including natural pandemics, earthquakes, landslides, heavy rainfall, long-term water supply vulnerability, tipping-points of ecosystem collapse, cyanobacterial bloom outbreaks, and droughts. === Economic and social challenges === The University of Southern California launched the Center for Artificial Intelligence in Society, with the goal of using AI to address problems such as homelessness. Stanford researchers use AI to analyze satellite images to identify high poverty areas. == Entertainment and media == === Media === AI applications analyze media content such as movies, TV programs, advertisement videos or user-generated content. The solutions often involve computer vision. Typical scenarios include the analysis of images using object recognition or face recognition techniques, or the analysis of video for scene recognizing scenes, objects or faces. AI-based media analysis can facilitate media search, the creation of descriptive keywords for content, content policy monitoring (such as verifying the suitability of content for a particular TV viewing time), speech to text for archival or other purposes, and the detection of logos, products or celebrity faces for ad placement. Motion interpolation Pixel-art scaling algorithms Image scaling Imag
Deep learning in photoacoustic imaging
Photoacoustic imaging (PA) is based on the photoacoustic effect, in which optical absorption causes a rise in temperature, which causes a subsequent rise in pressure via thermo-elastic expansion. This pressure rise propagates through the tissue and is sensed via ultrasonic transducers. Due to the proportionality between the optical absorption, the rise in temperature, and the rise in pressure, the ultrasound pressure wave signal can be used to quantify the original optical energy deposition within the tissue. Photoacoustic imaging has applications of deep learning in both photoacoustic computed tomography (PACT) and photoacoustic microscopy (PAM). PACT utilizes wide-field optical excitation and an array of unfocused ultrasound transducers. Similar to other computed tomography methods, the sample is imaged at multiple view angles, which are then used to perform an inverse reconstruction algorithm based on the detection geometry (typically through universal backprojection, modified delay-and-sum, or time reversal ) to elicit the initial pressure distribution within the tissue. PAM on the other hand uses focused ultrasound detection combined with weakly focused optical excitation (acoustic resolution PAM or AR-PAM) or tightly focused optical excitation (optical resolution PAM or OR-PAM). PAM typically captures images point-by-point via a mechanical raster scanning pattern. At each scanned point, the acoustic time-of-flight provides axial resolution while the acoustic focusing yields lateral resolution. == Applications of deep learning in PACT == The first application of deep learning in PACT was by Reiter et al. in which a deep neural network was trained to learn spatial impulse responses and locate photoacoustic point sources. The resulting mean axial and lateral point location errors on 2,412 of their randomly selected test images were 0.28 mm and 0.37 mm respectively. After this initial implementation, the applications of deep learning in PACT have branched out primarily into removing artifacts from acoustic reflections, sparse sampling, limited-view, and limited-bandwidth. There has also been some recent work in PACT toward using deep learning for wavefront localization. There have been networks based on fusion of information from two different reconstructions to improve the reconstruction using deep learning fusion based networks. === Using deep learning to locate photoacoustic point sources === Traditional photoacoustic beamforming techniques modeled photoacoustic wave propagation by using detector array geometry and the time-of-flight to account for differences in the PA signal arrival time. However, this technique failed to account for reverberant acoustic signals caused by acoustic reflection, resulting in acoustic reflection artifacts that corrupt the true photoacoustic point source location information. In Reiter et al., a convolutional neural network (similar to a simple VGG-16 style architecture) was used that took pre-beamformed photoacoustic data as input and outputted a classification result specifying the 2-D point source location. ==== Deep learning for PA wavefront localization ==== Johnstonbaugh et al. was able to localize the source of photoacoustic wavefronts with a deep neural network. The network used was an encoder-decoder style convolutional neural network. The encoder-decoder network was made of residual convolution, upsampling, and high field-of-view convolution modules. A Nyquist convolution layer and differentiable spatial-to-numerical transform layer were also used within the architecture. Simulated PA wavefronts served as the input for training the model. To create the wavefronts, the forward simulation of light propagation was done with the NIRFast toolbox and the light-diffusion approximation, while the forward simulation of sound propagation was done with the K-Wave toolbox. The simulated wavefronts were subjected to different scattering mediums and Gaussian noise. The output for the network was an artifact free heat map of the targets axial and lateral position. The network had a mean error rate of less than 30 microns when localizing target below 40 mm and had a mean error rate of 1.06 mm for localizing targets between 40 mm and 60 mm. With a slight modification to the network, the model was able to accommodate multi target localization. A validation experiment was performed in which pencil lead was submerged into an intralipid solution at a depth of 32 mm. The network was able to localize the lead's position when the solution had a reduced scattering coefficient of 0, 5, 10, and 15 cm−1. The results of the network show improvements over standard delay-and-sum or frequency-domain beamforming algorithms and Johnstonbaugh proposes that this technology could be used for optical wavefront shaping, circulating melanoma cell detection, and real-time vascular surgeries. === Removing acoustic reflection artifacts (in the presence of multiple sources and channel noise) === Building on the work of Reiter et al., Allman et al. utilized a full VGG-16 architecture to locate point sources and remove reflection artifacts within raw photoacoustic channel data (in the presence of multiple sources and channel noise). This utilization of deep learning trained on simulated data produced in the MATLAB k-wave library, and then later reaffirmed their results on experimental data. === Ill-posed PACT reconstruction === In PACT, tomographic reconstruction is performed, in which the projections from multiple solid angles are combined to form an image. When reconstruction methods like filtered backprojection or time reversal, are ill-posed inverse problems due to sampling under the Nyquist-Shannon's sampling requirement or with limited-bandwidth/view, the resulting reconstruction contains image artifacts. Traditionally these artifacts were removed with slow iterative methods like total variation minimization, but the advent of deep learning approaches has opened a new avenue that utilizes a priori knowledge from network training to remove artifacts. In the deep learning methods that seek to remove these sparse sampling, limited-bandwidth, and limited-view artifacts, the typical workflow involves first performing the ill-posed reconstruction technique to transform the pre-beamformed data into a 2-D representation of the initial pressure distribution that contains artifacts. Then, a convolutional neural network (CNN) is trained to remove the artifacts, in order to produce an artifact-free representation of the ground truth initial pressure distribution. ==== Using deep learning to remove sparse sampling artifacts ==== When the density of uniform tomographic view angles is under what is prescribed by the Nyquist-Shannon's sampling theorem, it is said that the imaging system is performing sparse sampling. Sparse sampling typically occurs as a way of keeping production costs low and improving image acquisition speed. The typical network architectures used to remove these sparse sampling artifacts are U-net and Fully Dense (FD) U-net. Both of these architectures contain a compression and decompression phase. The compression phase learns to compress the image to a latent representation that lacks the imaging artifacts and other details. The decompression phase then combines with information passed by the residual connections in order to add back image details without adding in the details associated with the artifacts. FD U-net modifies the original U-net architecture by including dense blocks that allow layers to utilize information learned by previous layers within the dense block. Another technique was proposed using a simple CNN based architecture for removal of artifacts and improving the k-wave image reconstruction. ==== Removing limited-view artifacts with deep learning ==== When a region of partial solid angles are not captured, generally due to geometric limitations, the image acquisition is said to have limited-view. As illustrated by the experiments of Davoudi et al., limited-view corruptions can be directly observed as missing information in the frequency domain of the reconstructed image. Limited-view, similar to sparse sampling, makes the initial reconstruction algorithm ill-posed. Prior to deep learning, the limited-view problem was addressed with complex hardware such as acoustic deflectors and full ring-shaped transducer arrays, as well as solutions like compressed sensing, weighted factor, and iterative filtered backprojection. The result of this ill-posed reconstruction is imaging artifacts that can be removed by CNNs. The deep learning algorithms used to remove limited-view artifacts include U-net and FD U-net, as well as generative adversarial networks (GANs) and volumetric versions of U-net. One GAN implementation of note improved upon U-net by using U-net as a generator and VGG as a discriminator, with the Wasserstein metric and gradient penalty to stabilize training (WGAN-GP). ==== Pixel-wise interpolation
Ontology for Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL). As of March 2008, a pre-release version of the ontology was made available at the project's SVN repository. == Scope == The Ontology for Biomedical Investigations (OBI) addresses the need for controlled vocabularies to support integration and joint ("cross-omics") analysis of experimental data, a need originally identified in the transcriptomics domain by the FGED Society, which developed the MGED Ontology as an annotation resource for microarray data.Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. (November 2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–5. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687. OBI uses the basic formal ontology upper-level ontology as a means of describing general entities that do not belong to a specific problem domain. As such, all OBI classes are a subclass of some BFO class. The ontology has the scope of modeling all biomedical investigations and as such contains ontology terms for aspects such as: biological material – for example blood plasma instrument (and parts of an instrument therein) – for example DNA microarray, centrifuge information content – such as an image or a digital information entity such as an electronic medical record design and execution of an investigation (and individual experiments therein) – for example study design, electrophoresis material separation data transformation (incorporating aspects such as data normalization and data analysis) – for example principal components analysis dimensionality reduction, mean calculation Less 'concrete' aspects such as the role a given entity may play in a particular scenario (for example the role of a chemical compound in an experiment) and the function of an entity (for example the digestive function of the stomach to nutriate the body) are also covered in the ontology. == OBI consortium == The MGED Ontology was originally identified in the transcriptomics domain by the FGED Society and was developed to address the needs of data integration. Following a mutual decision to collaborate, this effort later became a wider collaboration between groups such as FGED, PSI and MSI in response to the needs of areas such as transcriptomics, proteomics and metabolomics and the FuGO (Functional Genomics Investigation Ontology) was created. This later became the OBI covering the wider scope of all biomedical investigations. As an international, cross-domain initiative, the OBI consortium draws upon a pool of experts from a variety of fields, not limited to biology. The current list of OBI consortium members is available at the OBI consortium website. The consortium is made up of a coordinating committee which is a combination of two subgroups, the Community Representative (those representing a particular biomedical community) and the Core Developers (ontology developers who may or may not be members of any single community). Separate to the coordinating committee is the Developers Working Group which consists of developers within the communities collaborating in the development of OBI at the discretion of current OBI Consortium members. == Papers on OBI ==